RNA Replication Using Transcription Polymerases

ABSTRACT

Compositions and methods for amplifying RNA by replication using transcription polymerases are disclosed. Such replicated RNAs can be used in various applications such as RNAi therapeutics, diagnostic probes, RNA sequencing, directed evolution of RNA aptamers without intermediate conversion to DNA, and RNA vaccines. The transcription polymerases comprise T7 bacteriophage RNA polymerase.

FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was made with Government support under contract GM37706 awarded by the National Institutes of Health. The Government has certain rights in the invention.

BACKGROUND

Transcription polymerases (DNA-dependent RNA polymerases) mediate information transfer from DNA to RNA across the tree of life. In addition to their expected activity to linearly amplify RNA from DNA templates, some transcription polymerases can also exponentially replicate particular RNA templates, as has been demonstrated in vitro for transcription polymerases from Escherichia coli (Biebricher et al. (1973) Proc. Natl. Acad. Sci. 70:934-938, Wettich et al. (2001) Biochemistry 40:3308-3315) and bacteriophage T7 (Konarska et al. (1989) Cell 57:423-431, Konarska et al. (1990) Cell 63:609-618, Biebricher et al. (1996) EMBO J. 15:3458-3465, Kakimoto et al. (2015) AIP Conf. Proc. 1649:113-115). By RNA replication is meant a template-regenerating process that includes (i) full-length copying of an RNA template followed by (ii) the resulting RNA copy serving as template for new synthesis of full-length RNA copies. Importantly, such an RNA replication process does not involve DNA.

Historically, the transcription polymerase of T7 bacteriophage (T7 RNAP) has served as a model enzyme for its DNA-dependent RNA polymerase activity (Steitz (2004) Curr. Opin. Struct. Biol. 14:4-9). T7 RNAP also provides a paradigm for investigating RNA replication by transcription polymerases at the molecular level (Konarska et al. (1989), supra; Konarska et al. (1990), supra; Biebricher, et al. (1996), supra). Of note, a chloroplastic transcription polymerase similar to T7 RNAP may be the enzyme that replicates ASBVd, the canonical member of the Avsunviroidae family of viroids (Navarro et al. (2000) Virology 268:218-225).

There remains a need for improved methods of producing RNA for various applications.

SUMMARY

The present invention is based, in part, on the discovery that RNA can be replicated using transcription polymerases. Thus, the present disclosure further pertains to compositions and methods for replicating RNAs of interest for use in various applications such as RNAi therapeutics, diagnostic probes, RNA sequencing, directed evolution of RNA aptamers without intermediate conversion to DNA, and RNA vaccines.

In one aspect, a method of amplifying RNA is provided, the method comprising replicating the RNA in a reaction mixture comprising an RNA polymerase; a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, or analogues or derivatives thereof; and an RNA template comprising (i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat.

In certain embodiments, the transcription polymerase is a bacteriophage transcription polymerase, for example, including without limitation a T7 bacteriophage RNA polymerase such as encoded by gene 1 of the T7 bacteriophage.

In some embodiments, the reaction mixture contains no DNA.

In other embodiments, a method of amplifying RNA is provided, the method comprising replicating the RNA in a reaction mixture comprising: an RNA polymerase; a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, or analogues or derivatives thereof; and a DNA seed, wherein an RNA template for replication is generated by transcription of the DNA seed. In some embodiments, the DNA seed comprises a nucleotide sequence of interest and a 4-way repeat unit. In certain embodiments, the DNA seed is added to the reaction mixture such that the RNA polymerase generates a first RNA comprising the 4-way repeat unit by transcription of the DNA seed. In some embodiments, the method further comprises carrying out a first round of 3′-extension of the first RNA to produce a second RNA comprising a second 4-way repeat unit; and carrying out a second round of 3′-extension of the second RNA to produce the RNA template comprising the 4-way repeat configuration.

In certain embodiments, the RNA template ranges from 50 to 120 nucleotides in length.

In certain embodiments, each repeat region within the 2-way repeat configuration ranges from 10 to 60 nucleotides in length, or any length within this range such as 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 nucleotides in length. In certain embodiments, each repeat region within the 2-way repeat configuration ranges from about 20% to about 50% of the total length of the replicating RNA, or any length within this range such as 20%, 22%, 23%, 24%, 26%, 28%, 30%, 32%, 34%, 36%, 38%, 40%, 42%, 44%, 46%, 48%, or 50% of the total length of the replicating RNA.

In certain embodiments, each repeat region within the 4-way repeat configuration ranges from about 5 to about 25 nucleotides in length, or any length within this range such as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In certain embodiments, each repeat region within the 4-way repeat configuration ranges from about 5% to about 20% of the total length of the replicating RNA, or any length within this range such as 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20% of the total length of the replicating RNA.

In certain embodiments, the replicating RNA in the reaction comprises a G RNA strand comprising two G bases at or close to the 5′ end and two G bases at or close to the 3′ end, and a complementary C RNA strand comprising two C bases at or close to the 5′ end and two C bases at or close to the 3′ end.

In certain embodiments, the method further comprises adding at least one base to the 3′ ends of the G RNA strand or the C RNA strand. In some embodiments, an adenine base is added to the 3′ end of the G RNA strand or the C RNA strand. In some embodiments, one to three bases are added to the 3′ end of the G RNA strand or the C RNA strand.

In certain embodiments, the RNA template is linear.

In certain embodiments, a single RNA or a plurality of RNAs are replicated in the reaction mixture. In some embodiments, the plurality of RNAs are RNA variants.

In certain embodiments, the methods described herein are performed in a microfluidic device. In some embodiments, the microfluidic device comprises a droplet generator. In some embodiments, the method further comprises partitioning a plurality of RNAs into a plurality of droplets. In some embodiments, the RNA is replicated using digital droplet RNA replication.

In certain embodiments, the method further comprises using the amplified RNA for RNA interference, sequencing, expression profiling, a vaccine, or directed evolution of RNA aptamers without intermediate conversion to DNA.

In certain embodiments, the replicating RNA comprises a nucleotide sequence selected from Tables 1, 2, or 4, or a sequence displaying at least about 80-100% sequence identity thereto, including any percent identity within this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% sequence identity thereto. In some embodiments, the replicating RNA comprises i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat. In some embodiments, the RNA template comprises a G RNA strand comprising two G bases at or close to a 5′ end and two G bases at or close to a 3′ end of the G RNA strand, or a C RNA strand comprising two C bases at or close to a 5′ end and two C bases at or close to a 3′ end of the C RNA strand.

In certain embodiments, the method further comprises isolating a replicated RNA from the reaction mixture.

In certain embodiments, the method further comprises substantially purifying a replicated RNA from the reaction mixture.

In certain embodiments, the RNA polymerase is at concentration of at least about 1 nM in the reaction mixture.

In another aspect, a composition for generating replicating RNA templates is provided, the composition comprising: a) an RNA template for RNA replication, wherein the RNA template comprises (i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat; b) an RNA polymerase; c) a DNA seed comprising a nucleotide sequence of interest and a 4-way repeat unit; and d) a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, or analogues or derivatives thereof. In some embodiments, the set of ribonucleoside triphosphates further comprises a modified nucleotide or nucleotide analogue.

In another aspect, a composition for generating replicating RNA templates is provided, the composition comprising: a) an RNA polymerase; b) a DNA seed; and c) a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, or analogues or derivatives thereof. In some embodiments, the DNA seed comprises a nucleotide sequence of interest and a 4-way repeat unit.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is best understood from the following detailed description when read in conjunction with the accompanying drawings. The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. It is emphasized that, according to common practice, the various features of the drawings are not to-scale. On the contrary, the dimensions of the various features are arbitrarily expanded or reduced for clarity. Included in the drawings are the following figures.

FIGS. 1A-1G show diverse but structurally-similar RNAs isolated from no-template-added, high concentration T7 RNA polymerase (T7 RNAP) reactions set up in parallel. FIG. 1A) Experimental scheme. No DNA or RNA template was explicitly added to any reaction. FIG. 1B) Representative denaturing gel image illustrates the different migration of products from no-template T7 RNAP reactions that had been set up in parallel. M=marker (denatured 10 base-pair DNA ladder), nt=nucleotides. FIG. 1C) Results from high-throughput sequencing of 24 reactions which were set up in parallel. Sequenced pools were dominated by 1 to 3 RNA species, with a species referring to a heterogenous population of closely related RNA sequences. RNA species constituting >5% of any sequenced pool are depicted. FIG. 1D) Sequence diversity of RNA species. “Reference sequence” for each RNA species refers to a canonical, abundant sequence defining the species. Also depicted is the relation of reference sequences to Y RNA, a previously characterized sequence that can be replicated by T7 RNAP (Konarska et al. Cell 63, 609-618 (1990)). FIG. 1E) Length distribution of reference sequences. FIG. 1F) RNA species are constituted by sequences of both strand orientations. Plot shows fraction of reads from each reaction aligning to the canonical reference sequences (x axis) and to their reverse complements (y axis). Diagonal lines (0.5:1, 1:1 and 2:1) are shown as visual aids. FIG. 1G) Structural similarity of RNA species. Arrows denote 2-way- and 4-way-repeats. Arrows of the same length pointing in opposite directions denote complementary repeats. Five representative examples of RNA species are shown, along with 2-way- and 4-way-repeats. Prime (′) denotes reverse complement of reference sequence for a species. Histograms quantify 2-way- and 4-way-repeat lengths for all RNA species. FIGS. 1C-1F follow the same color coding for RNA species.

FIGS. 2A-2B show 3′ base additions to the G and C strand templates are required for efficient RNA synthesis. FIG. 2A) Gel-based assay showing increased T7 RNAP reaction products after T4 RNA ligase 1 (T4Rnl1)-catalyzed addition of pAp (adenosine 3′,5′-diphosphate) to the Y2 RNA G and C strands. M=marker (denatured 10 base-pair DNA ladder), nt=nucleotides, ng=nanograms. All gels were processed in parallel. Bar plot shows background-subtracted average gel intensity for duplicate reactions for each experimental condition, with the whiskers representing the range of the duplicates. FIG. 2B) “Subterminal de novo initiation” model for RNA replication by T7 RNAP. N₊1 denotes one or a few extra bases at the 3′ end. Light gray=G strand with 3′ extra bases, dark gray=C strand with 3′ extra bases.

FIGS. 3A-3C show that replicating RNA populations consist of multiple replication-competent sequences. (FIG. 3A) Test of the hypothesis that RNAs with sequence variation compared to the reference sequence can also be replicated. Copying of RNAs with sequence variation is expected to result in complementary sequence variant profiles for the two replicating RNA strands. The degree of complementarity may be quantitatively assessed using the sample Pearson correlation coefficient. Plots in (FIG. 3B) and (FIG. 3C) show the distribution of sequence variants for two amplified RNA populations: FIG. 3B) RNA species obtained from a templated T7 RNAP reaction starting with the chemically synthesized Y2 RNA G strand with an extra 3′ adenine, and FIG. 3C) RNA species 2.1 from FIG. 1. Frequencies at which sequence variants were detected are shown per position for three distinct types of variants: transitions (A->G, C->U, G->A, U->C), transversions (A->C or U, C->A or G, G->C or U, U->A or G) and single-base deletions. Symmetry between the sequence variants (complementary variation) on the two strands and values close to 1 for the sample Pearson correlation coefficient support the hypothesis that templates bearing sequence variants can be replicated by T7 RNAP. 95% confidence intervals for the sample Pearson correlation coefficient were estimated by non-parametric bootstrapping to be 0.76-0.96 for the RNA population in (FIG. 3B) and 0.96-0.999 for the population in (FIG. 3C).

FIGS. 4A-4D show that 2-way- and 4-way-repeat configurations are required for efficient replication of X and Y2 RNA. Six degenerate libraries (X₁-X₄, Y2₁-Y2₂) were constructed by randomizing the base identities at a subset of sequence positions in either X RNA or Y₂ RNA. G strand sequences for X and Y2 RNA are shown, with putative 2-way- (blue) and 4-way- (orange) repeats. X RNA has an imperfect 4-way repeat (vertical orange bars show sequence insertions). Positions chosen for base randomization in X RNA and Y2 RNA are listed below the degenerate library names in FIGS. 4A-4C. Degenerate libraries were used as templates in T7 RNAP reactions, and RNA populations before replication (represented by “I”) and after replication (represented by “0”) were sequenced. FIG. 4A) 2-way repeat requirement was tested by randomizing bases at two potentially base pairing positions in the 2-way repeat (but outside the 4-way repeat). FIG. 4B) 4-way repeat requirement was tested by randomizing bases at four potentially base pairing positions in the 4-way repeat. Post-replication, a limited diversity of FIG. 4A) 2 base- and FIG. 4B) 4 base-combinations was dominant at the randomized base positions. FIG. 4C) The X4 mutant library contained randomized bases at only two of the four potentially base pairing positions in the 4-way repeat. Post-replication, only the 2 base combination (C, G) was dominant at the randomized base positions leading to the 4 base Watson-Crick combination (G,C,G,C) in the 4-way repeat. In panels (FIGS. 4A-4C), the different Watson-Crick base combinations are shown by unique colors. An abundant non-Watson-Crick base combination (>1% relative abundance within the sequenced pool) is shown individually in gray. Infrequent non-Watson-Crick base combinations (<1% individual relative abundance within the sequenced pool) are summed together and shown in white. FIG. 4D) Shape-shifting model. The 2-way repeat requirement (panel A) evidences a long hairpin RNA secondary structure whereas the 4-way repeat requirement (FIGS. 4B and 4C) evidences an alternative RNA secondary structure which is also important over the course of replication.

FIGS. 5A-5E show that T7 RNAP can use the same template molecule processively to instruct multiple rounds of RNA synthesis. RNA dimers containing two full-length repeats of the template sequence are synthesized in T7 RNAP reactions initiated with single-copy RNA templates (RNA monomers). FIG. 5A) Two possible types of mechanisms for RNA dimer synthesis: uni-templated and bi-templated. A uni-templated mechanism involves the same monomer molecule templating synthesis of each half of the RNA dimer. A bi-templated mechanism involves two different monomer template molecules templating synthesis of each half of the dimer. FIG. 5B) Experimental scheme to assess RNA dimer synthesis. When RNA dimers are obtained using a diversity of monomer templates in the same T7 RNAP reaction, uni- and bi-templated mechanisms have distinct predictions for sequence agreement between the two halves of RNA dimers (half 1=half 2 for uni-templated synthesis; half 1=half 2 in proportion to the template concentration for bi-templated synthesis). Experiments were performed in duplicate with each of two starting diverse monomer pools, X₁ and Y2₁. Each pool contained randomized bases at a distinct set of six positions. Base identities at these six positions were used for calculating sequence agreement between the two dimer halves. FIG. 5C) Observed sequence agreement between the two dimer halves by analyzing all dimers together in bulk. FIG. 5D) Observed sequence agreement between the two dimer halves by analyzing dimers individually for the 10 most abundant RNA templates present in the sequenced pools. No mismatches were allowed in calculation of sequence agreement for panels (FIG. 5C) and (FIG. 5D). The strong sequence concordance between the dimer halves (panels (FIG. 5C) and (FIG. 5D)) supports uni-templated synthesis as the dominant mechanism for RNA dimer synthesis. FIG. 5E) Model for uni-templated synthesis is in effect an interrupted rolling circle mechanism involving linear rather than circular templates.

FIGS. 6A-6F show the origin of replicating RNAs via molecular evolution. FIG. 6A) Some RNA species from no-template-added T7 RNAP reactions match known genomes. An example RNA species matching the human genome is shown. p-value is based on alignment to the RefSeq genomic database. The long hairpin shown is a predicted structure. Convention for annotating RNAs: (i) Best match to a known genome is shown in a red box; (ii) 4-way repeats are shown as orange arrows, with orange asterisks indicating sequence disagreements between 4-way repeats; (iii) Long 2-way repeats, though present, are not shown for simplicity. FIG. 6B) Experimental schematic to test the hypothesis that replicating RNAs can originate through partial instruction from DNA seeds. A complex DNA pool (consisting of DNA derived from three nematode species, yeast, coliphage lambda and a plasmid) was used to seed high concentration T7 RNAP reactions. Controls performed in parallel were (i) Unseeded, (ii) Seeded with DNase-treated DNA pool, and (iii) Seeded with hot alkali-treated DNA pool. Bulk tube- and microfluidic drop-reactions were set up in parallel for each experimental condition, followed by RNA-Seq and bioinformatic analysis. FIG. 6C) Scatter plots show results of alignment of RNA species (individual points) to our designed DNA seed pool (y axis) and to all available RefSeq genome assemblies excluding those in our DNA seed pool (x axis). RNA species with strong sequence matches to input DNA seeds (upper left regions of scatter plots) were specifically observed for reactions seeded with the DNA pool or the hot alkali-treated DNA pool compared to the two negative controls (unseeded reactions and reactions seeded with DNase-treated DNA pool). 220 RNA species are shown on the left scatter plot, and 204 on the right scatter plot. For each seeded or unseeded condition, RNA species from two different aggregated drop reactions (corresponding to two time points) are shown together on scatter plots. FIG. 6D) Histogram shows relative locations of seed matches and 4-way repeats for RNA species from aggregated drop reactions seeded with the DNA pool or the hot alkali-treated DNA pool. RNA species with >=26 bases matching to our DNA pool were used for the histogram because matches in this length range were absent for RNA species from the negative controls. Seed matches start close to either 5′ or 3′ end of replicating RNAs and extend up to the second 4-way repeat unit that is encountered from the start of the match. FIG. 6E) Examples of RNA species that originated from different sources in our designed DNA pool. The shown RNA species were all isolated from drop reactions, either from the “Seeded with DNA pool” condition or from the “Seeded with hot alkali-treated DNA pool” condition. Annotation of RNAs as in panel (A). p-values are based on alignment to a database consisting of sequences expected to be present in our DNA seed pool. FIG. 6F) Proposed mechanism for the origin of replicating RNAs.

FIG. 7 shows a schematic of the RNA-Seq protocol. Representative gel images at various steps of the protocol are shown. UMI=Unique Molecular Identifier (a degenerate 6- or 8-base molecular barcode), M=marker (denatured 10 base-pair DNA ladder), L=100 base-pair ladder, bp=base-pair, nt=nucleotides.

FIGS. 8A-8B show sustained and templated propagation of RNA species originally isolated from no-template-added, high concentration T7 RNAP reactions. FIG. 8A) Regeneration of RNA species upon dilution into fresh, low concentration T7 RNAP reactions. Gels for the (−) and (+) T7 RNAP reactions with the diluted Round 1 RNA pool as template were processed in parallel. nt=nucleotides. FIG. 8B) Templated growth of RNA species. Three Round 1 RNA pools (originally isolated from no-template-added reactions) were propagated in parallel. The Round 2 products from a particular reaction corresponded in sequence to the Round 1 RNA pool used as template for that reaction. Sequences for the most abundant RNA species in the three Round 2 pools are listed in Table 4.

FIG. 9 shows pervasive addition of bases at the 3′ end in RNA species from no-template-added reactions. RNA species from FIG. 1 further analyzed here. For each RNA reference sequence (first bar for each RNA species) and its reverse complement (second bar), the percentage of reads terminating (at positions −2, −1 and 0 from the 3′ end) without further base additions (“No 3′ base addition” in gray) is shown alongside the percentage of reads terminating with base additions (“3′ base addition” in navy).

FIGS. 10A-10C show the role of 3′ base additions in RNA replication by T7 RNAP. FIG. 10A) Gel-based assay showing increased T7 RNAP reaction products after chemical addition of a single adenine or uracil to the 3′ ends of the Y2 RNA G and C strands. M=marker (denatured 10 base-pair DNA ladder), nt=nucleotides, ng=nanograms. All gels were processed in parallel. Bar plot shows background—subtracted average gel intensity for duplicate reactions for each experimental condition, with the whiskers representing the range of the duplicates. FIG. 10B) The RNA 5′ chemical end partly accounts for differences in electrophoretic mobility between Y2 RNA replication products (5′-triphosphate) and chemically synthesized Y2 RNA oligos (5′-hydroxyl). RppH=RNA 5′ Pyrophosphohydrolase, SAP=Shrimp Alkaline Phosphatase, M=marker (denatured 10 base-pair DNA ladder), nt=nucleotides, OH=hydroxyl. FIG. 10C) Sequence distributions at 5′ ends of Y2 RNA synthetic oligos and Y2 RNA replication products. Complementary strand products (e.g. G strand products of CC-CCA template or C strand products of GG-GGA template) do not evidence 5′ uracil above background levels observed for synthetic oligos, supporting a subterminal initiation model over terminal initiation. A background of 5′ extensions in the detected sequences was expected from reverse transcriptase activity during RNA-seq library preparation. RT=reverse transcriptase.

FIGS. 11A-11B show a sequencing-based readout showing a key signature of RNA replication: synthesis of RNA molecules of both strand orientations in the same reaction starting with FIG. 11A (left) chemically synthesized Y2 RNA G strand with an extra 3′ adenine or FIG. 11A (right) chemically synthesized Y2 RNA C strand with an extra 3′ adenine. nt=nucleotides. FIG. 11B shows a schematic to explain how newly synthesized RNA products of both strand orientations can be identified in the same T7 RNAP reaction.

FIG. 12 shows further evidence for uni-templated synthesis being the dominant mechanism for generation of RNA dimers. In the schematic at the top, blue- and red-colored bars represent different sequences which may have one or more mismatches with respect to each other. Data shown are for dimers obtained starting with the diverse monomer template pools X₁ and Y2₁. Individual dimer sequences are plotted at different coordinates along the x axis. The vast majority of dimer sequences were concordant, i.e. had perfect sequence agreement between the first and second dimer halves. The observed counts for these concordant dimers are shown in the left plots (each blue dot represents a particular dimer sequence), along with a range of counts expected from bi-templated synthesis generating the concordant dimers (yellow area). The consistent overrepresentation of observed concordant dimer counts over expected counts, across a diversity of dimer sequences, supports a uni-templated mechanism. Conversely, such overrepresentation was not observed when analysis was performed on the small fraction of dimer sequences where there was sequence disagreement between the first and second dimer halves (plots on the right).

FIGS. 13A-13B show that uni-templated synthesis of RNA dimers is further supported by concordance of sequence variants between dimer halves. RNA dimers were obtained starting with the diverse monomer template pools X₁ and Y2₁; each pool contained intentionally randomized bases at a distinct set of six positions (denoted by “N”). For this figure, sequence variants refer to polymorphisms in RNA dimers located outside the intentionally randomized bases. FIG. 13A) Plots on the left show analysis for the vast majority of dimers with perfect sequence agreement between the six randomized base positions in the two dimer halves. For such dimers, the observed concurrent incidence of the same sequence variants in both dimer halves (red bars) was more frequent by 4.5 fold (X₁ pool) or 7 fold (Y2₁ pool) compared to the null hypothesis* (blue bars). Conversely, increased concurrent incidence of sequence variants compared to the null hypothesis* was not evident when analysis was performed on the small fraction of dimer sequences with sequence disagreement between the six randomized base positions in the two dimer halves (plots on the right). *=Null hypothesis was that sequence variants occur concurrently by random chance based on the frequencies of the sequence variants in the population. FIG. 13B) Concurrent incidence of sequence variants for an example RNA template from the X₁ pool. G strand sequence of the example template shown in blue and C strand sequence in green. The “N” in purple above the sequences shows the positions of intentionally randomized bases in the X₁ pool.

FIGS. 14A-14B show an analysis of the junction sequences between the two halves of the RNA dimers. FIG. 14A) Observed sequence agreement between the dimer junction and 3′ end (purple bars in left plot) was close to what would be expected based on the junction sequence distribution and 3′ end sequence distribution being independent of each other (mustard bars in left plot). Data shown are for dimers obtained starting from both the X₁ and Y2₁ diverse RNA monomer pools. Each pool contained intentionally randomized bases at a distinct set of six positions. Dimers used for analysis here had perfect sequence agreement between the six randomized base positions in the two dimer halves. The greater-than-expected concordance of sequence variants (located outside the intentionally randomized bases) between RNA dimer halves served as an internal positive control (based on FIG. 13 results) for our sequence agreement calculations (right plot). FIG. 14B) Dimer junction and 3′ end sequences for an example RNA template from the X₁ pool. G strand sequence of the example template shown in dark gray and C strand sequence in light gray.

FIG. 15 shows microfluidic drop generation setup for T7 RNAP-catalyzed RNA replication reactions. One reagent stream was used to flow in nucleoside triphosphates (NTPs) and when stated, RNA or DNA templates. The other reagent stream was used to flow in T7 RNAP.

FIG. 16 shows migration of aggregated drop reactions on denaturing gels. Reactions were conducted at high concentration of T7 RNAP. Aggregated drop reactions shown correspond to: (i) no-template-added (reaction 1), (ii) seeded with a DNA pool consisting of DNA from nematodes, yeast, phage and a plasmid (reaction 2), and (iii) seeded with the DNA pool, with the DNA pool having been pre-treated with DNase (reaction 3).

FIG. 17 shows digital droplet RNA replication. Chemically synthesized G strand of Y2 RNA with an extra 3′ adenine was used as template. Reactions were conducted at low concentration of T7 RNAP. Bright, fluorescent drops evidence RNA replication. % drops fluorescent reported as (Mean+/−Standard deviation). If replication could proceed starting with a single template molecule, then using the measurements obtained with the 3.31 template copies/drop condition, the % drops fluorescent predicted by Poisson statistics for the 0.39 copies/drop condition would be 5.2+/−0.6, close to the observed value of 6.6+/−1.1. In contrast, if replication could only proceed starting with two or more template molecules, the % drops fluorescent predicted for the 0.39 copies/drop condition would be 1.0+/−0.1, which deviates from observation.

FIG. 18 shows novel replicating RNAs can be isolated from no-template-added, high concentration T7 RNAP reactions set up in microfluidic droplets. A gel-extracted sample of aggregated drop reactions (Round 1 RNA pool) was used in bulk as template in a 10 μl low concentration T7 RNAP reaction (products called Round 2 RNA pool). Both Round 1- and Round 2-RNA pools were characterized by RNA-Seq. As expected from competition between RNA species during amplification of the Round 1 pool, most RNA species from the Round 1 pool were not detected in the Round 2 pool. The predominance in the Round 2 pool of a small subset of species from the Round 1 pool demonstrates the capability of this subset of species to replicate (and to survive by out-competing other species). Furthermore, the predominant species in the Round 2 pool exhibited typical sequence and structural hallmarks of RNAs replicated by T7 RNAP (e.g. 2-way repeats and 4-way repeats). The top five most abundant RNA species in the Round 2 pool are shown as examples. Arrows above each RNA sequence represent 2-way- and 4-way-repeats, with vertical bars along the arrows indicating sequence disagreements between the repeats.

FIG. 19 shows evolution of RNA sequences similar to the T7rp1 replicating RNA reported by Biebricher and Luce (EMBO J. 15, 3458-3465 (1996)). Bases matching in alignments to T7rp1 are shown in red. Sequences with the same strand orientation as T7rp1 are assigned polarity (“P”) of plus (+); sequences complementary to T7rp1 are assigned polarity of minus (−). T7rp1 strongly matches the cow and yak genomes. The 10 RNA sequence examples shown were isolated as follows. First, we generated no-template-added, high concentration T7 RNAP drop reactions. Bovine serum albumin (BSA) was included in the reactions during drop generation. An aggregate of drop reactions was then used in bulk as template in a 10 μl low concentration T7 RNAP tube reaction. Sequences shown were products of this second-round tube reaction.

FIGS. 20A-20B show RNAs replicated by T7 RNAP can originate through partial instruction from DNA seeds. FIG. 20A) An example RNA species from a no-template-added T7 RNAP reaction matching the genome of Lactococcus lactis is shown. This panel supplements FIG. 6A. p-value is based on alignment to the RefSeq genomic database. The long hairpin shown is a predicted structure. FIG. 20B) More examples of RNA species that originated from different sources in our designed DNA pool. This panel supplements FIG. 6E. With the exception of the third RNA listed in this panel, the shown RNA species were all isolated from drop reactions, either from the “Seeded with DNA pool” condition or from the “Seeded with hot alkali-treated DNA pool” condition. The third RNA example was isolated from a tube reaction for the “Seeded with hot alkali-treated DNA pool” condition. Convention for annotating RNAs: (i) Best match to a source genome is shown in a red box; (ii) 4-way repeats are shown as orange arrows, with orange asterisks indicating sequence disagreements between 4-way repeats; (iii) Long 2-way repeats, though present, are not shown for simplicity. p-values are based on alignment to a database consisting of sequences expected to be present in our DNA seed pool.

DETAILED DESCRIPTION OF EMBODIMENTS

Compositions and methods for amplifying RNA by replication using transcription polymerases are disclosed. Such replicated RNAs are useful in various applications including, without limitation, RNAi therapeutics, diagnostic probes, RNA sequencing, directed evolution of RNA aptamers without intermediate conversion to DNA, and RNA vaccines.

Before the present compositions and methods are described, it is to be understood that this invention is not limited to a particular method or composition described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limits of that range is also specifically disclosed. Each smaller range between any stated value or intervening value in a stated range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included or excluded in the range, and each range where either, neither or both limits are included in the smaller ranges is also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, some potential and preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. It is understood that the present disclosure supersedes any disclosure of an incorporated publication to the extent there is a contradiction.

As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present invention. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.

It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an RNA” includes a plurality of such RNAs and reference to “the RNA” includes reference to one or more RNAs and equivalents thereof, e.g. transcripts, tRNA, rRNA, mRNA, and non-coding RNA (e.g., miRNA, siRNA, shRNA, lncRNA) known to those skilled in the art, and so forth.

The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.

The term “about”, particularly in reference to a given quantity, is meant to encompass deviations of plus or minus five percent.

As used herein, a “biological sample” refers to a sample of cells, tissue, or fluid isolated from a prokaryotic or eukaryotic organism, including but not limited to, for example, blood, plasma, serum, fecal matter, urine, bone marrow, bile, spinal fluid, lymph fluid, sputum, ascites, bronchial lavage fluid, synovial fluid, samples of the skin, external secretions of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, organs, biopsies, and also samples of cells, including cells from bacteria, archaea, fungi, protists, plants, and animals as well as in vitro cell culture constituents, including but not limited to, conditioned media resulting from the growth of cells and tissues in culture medium, e.g., recombinant cells, and cell components, and also samples containing nucleic acids from viruses.

“Substantially purified” generally refers to isolation of a substance (compound, RNA, DNA, polynucleotide) such that the substance comprises the majority percent of the sample in which it resides. Typically in a sample, a substantially purified component comprises 50%, preferably 80%-85%, more preferably 90-95% of the sample. Techniques for purifying polynucleotides and polypeptides of interest are well-known in the art and include, for example, ion-exchange chromatography, affinity chromatography and sedimentation according to density.

By “isolated” is meant, when referring to a protein, polypeptide, or peptide, that the indicated molecule is separate and discrete from the whole organism with which the molecule is found in nature or is present in the substantial absence of other biological macro molecules of the same type. The term “isolated” with respect to a polynucleotide is a nucleic acid molecule devoid, in whole or part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences in association therewith; or a molecule disassociated from the chromosome.

The term “derived from” is used herein to identify the original source of a molecule but is not meant to limit the method by which the molecule is made which can be, for example, by chemical synthesis or recombinant means.

“Homology” refers to the percent identity between two polynucleotide or two polypeptide molecules. Two nucleic acid, or two polypeptide sequences are “substantially homologous” to each other when the sequences exhibit at least about 50% sequence identity, preferably at least about 75% sequence identity, more preferably at least about 80% 85% sequence identity, more preferably at least about 90% sequence identity, and most preferably at least about 95% 98% sequence identity over a defined length of the molecules. As used herein, substantially homologous also refers to sequences showing complete identity to the specified sequence.

In general, “identity” refers to an exact nucleotide to nucleotide or amino acid to amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Percent identity can be determined by a direct comparison of the sequence information between two molecules by aligning the sequences, counting the exact number of matches between the two aligned sequences, dividing by the length of the shorter sequence, and multiplying the result by 100. Readily available computer programs can be used to aid in the analysis, such as ALIGN, Dayhoff, M. O. in Atlas of Protein Sequence and Structure M. O. Dayhoff ed., 5 Suppl. 3:353 358, National biomedical Research Foundation, Washington, D.C., which adapts the local homology algorithm of Smith and Waterman Advances in Appl. Math. 2:482 489, 1981 for peptide analysis. Programs for determining nucleotide sequence identity are available in the Wisconsin Sequence Analysis Package, Version 8 (available from Genetics Computer Group, Madison, Wis.) for example, the BESTFIT, FASTA and GAP programs, which also rely on the Smith and Waterman algorithm. These programs are readily utilized with the default parameters recommended by the manufacturer and described in the Wisconsin Sequence Analysis Package referred to above. For example, percent identity of a particular nucleotide sequence to a reference sequence can be determined using the homology algorithm of Smith and Waterman with a default scoring table and a gap penalty of six nucleotide positions.

Another method of establishing percent identity in the context of the present invention is to use the MPSRCH package of programs copyrighted by the University of Edinburgh, developed by John F. Collins and Shane S. Sturrok, and distributed by IntelliGenetics, Inc. (Mountain View, Calif.). From this suite of packages, the Smith Waterman algorithm can be employed where default parameters are used for the scoring table (for example, gap open penalty of 12, gap extension penalty of one, and a gap of six). From the data generated the “Match” value reflects “sequence identity.” Other suitable programs for calculating the percent identity or similarity between sequences are generally known in the art, for example, another alignment program is BLAST, used with default parameters. For example, BLASTN and BLASTP can be used using the following default parameters: genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swiss protein+Spupdate+PIR. Details of these programs are readily available.

Alternatively, homology can be determined by hybridization of polynucleotides under conditions which form stable duplexes between homologous regions, followed by digestion with single stranded specific nuclease(s), and size determination of the digested fragments. DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (3^(rd) Edition, 2001); DNA Cloning, Vols I & 2. (edited by D. Glover, IRL Press, Oxford, 1985); Nucleic Acid Hybridization (edited by S. Lukyanov, Springer, 2007).

“Recombinant” as used herein to describe a nucleic acid molecule means a polynucleotide of genomic, cDNA, viral, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation, is not associated with all or a portion of the polynucleotide with which it is associated in nature. The term “recombinant” as used with respect to a protein or polypeptide means a polypeptide produced by expression of a recombinant polynucleotide. In general, the gene of interest is cloned and then expressed in transformed organisms, as described further below. The host organism expresses the foreign gene to produce the protein under expression conditions.

“Purified polynucleotide” refers to a polynucleotide of interest or fragment thereof which is essentially free, e.g., contains less than about 50%, preferably less than about 70%, and more preferably less than about at least 90%, of the protein with which the polynucleotide is naturally associated. Techniques for purifying polynucleotides of interest are well-known in the art and include, for example, disruption of the cell containing the polynucleotide with a chaotropic agent and separation of the polynucleotide(s) and proteins by ion-exchange chromatography, affinity chromatography and sedimentation according to density.

Replicating RNA

RNA templates that can be replicated by a transcription polymerase are typically linear and comprise (i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat. In some embodiments, the replicating RNA further comprises one strand comprising two G bases at or close to the 5′ end and two G bases at or close to the 3′ end (i.e., a G RNA strand), and a complementary RNA strand comprising two C bases at or close to the 5′ end and two C bases at or close to the 3′ end (i.e., a C RNA strand). In certain embodiments, at least one base is added to the 3′ end of the G RNA strand and/or the C RNA strand. In some embodiments, one to three bases are added to the 3′ end of the G RNA strand and/or the C RNA strand. For example, 1, 2, or 3 bases can be added to either the G RNA strand or the C RNA strand or both the G RNA strand and the C RNA strand. In one embodiment, an adenine base is added to the 3′ end of the G RNA strand and/or the C RNA strand.

In certain embodiments, the RNA template ranges from about 50 to about 120 nucleotides in length, including any length within this range such as 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 120 nucleotides in length.

In certain embodiments, each repeat region within the 2-way repeat configuration ranges from about 10 to about 60 nucleotides in length, or any length within this range such as 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 nucleotides in length. In certain embodiments, each repeat region within the 2-way repeat configuration ranges from about 20% to about 50% of the total length of the replicating RNA, or any length within this range such as 20%, 22%, 23%, 24%, 26%, 28%, 30%, 32%, 34%, 36%, 38%, 40%, 42%, 44%, 46%, 48%, or 50% of the total length of the replicating RNA.

In certain embodiments, each repeat region within the 4-way repeat configuration ranges from about 5 to about 25 nucleotides in length, or any length within this range such as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In certain embodiments, each repeat region within the 4-way repeat configuration ranges from about 5% to about 20% of the total length of the replicating RNA, or any length within this range such as 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20% of the total length of the replicating RNA.

Exemplary replicating RNAs are listed in Tables 1, 2, and 4 (see Examples). In certain embodiments, the replicating RNA comprises a nucleotide sequence selected from Tables 1, 2, or 4, or a sequence displaying at least about 80-100% sequence identity thereto, including any percent identity within this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% sequence identity thereto. In some embodiments, the replicating RNA comprises i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat.

The transcription polymerase used in RNA replication can be any RNA polymerase capable of catalyzing replication of an RNA template having this structural configuration. Transcription polymerases can be obtained, for example, from bacteria, archaea, eukaryotes, and viruses. Exemplary transcription polymerases include, without limitation, those from bacteriophages (e.g., T7, T3, and SP6), bacteria (e.g., Escherichia coli), and eukaryotic chloroplasts and mitochondria. In certain embodiments, the RNA polymerase is engineered to improve its capability in replicating RNA. For example, the RNA polymerase may be engineered to comprise one or more mutations that enhance its catalytic activity, improve thermal stability, enhance promoter clearance, and/or increase processivity. T7 RNA polymerases genetically engineered to increase thermal stability are commercially available, for example, from New England Biolabs (Ipswich, Mass.) and Toyobo U.S.A., Inc. (New York, N.Y.)

For replication, the RNA polymerase is added to a reaction mixture containing the RNA template and a set of ribonucleoside triphosphates to catalyze polymerization and replication of RNA. The set of ribonucleoside triphosphates will usually include ATP, CTP, UTP and GTP, but may also include one or more modified ribonucleoside triphosphates or non-natural ribonucleoside triphosphate analogues, which may be incorporated into the RNA during polymerization. Alternatively or additionally, nucleotides may be modified in the RNA product after replication of the RNA is completed.

Modified nucleotides may include one or more modifications to the ribose and/or the base of the nucleoside. Such modifications may include, for example, without limitation, acyl, amino acid, aminoacyl, aminoalkyl, amino, carboxymethyl, epoxycyclopentane, glycosyl, heavy atom, hydrocarbon, hydrogen, hydroxyalkyl, methoxycarbonyl, methyl, nucleobase, nucleotide, oxo, peroxide, phosphoribose, polyamine, saccharide, seleno, sulfur, and/or thioalkyl moieties.

Modified nucleotides may include, for example, without limitation 1,2′-O-dimethyladenosine, 1,2′-O-dimethylguanosine, 1,2′-O-dimethylinosine, 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine, 1-methyladenosine, 1-methylguanosine, 1-methylinosine, 1-methylpseudouridine, 2,8-dimethyladenosine, msms2i6A, 2-geranylthiouridine, 2-lysidine, 2-methyladenosine, 2-methylthio cyclic N6-threonylcarbamoyladenosine, 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine, 2-methylthio-N6-hydroxynorvalylcarbamoyladenosine, 2-methylthio-N6-isopentenyladenosine, 2-methylthio-N6-methyladenosine, 2-methylthio-N6-threonylcarbamoyladenosine, 2-selenouridine, 2-thio-2′-O-methyluridine, 2-thiocytidine, 2-thiouridine, 2′-O-methyladenosine, 2′-O-methylcytidine, 2′-O-methylguanosine, 2′-O-methylinosine, 2′-O-methylpseudouridine, 2′-O-methyluridine, 2′-O-methyluridine 5-oxyacetic acid methyl ester, 2′-O-ribosyladenosine (phosphate), 2′-O-ribosylguanosine (phosphate), 2′3′-cyclic phosphate end, hm5Cm, 3,2′-O-dimethyluridine, 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine, 3-(3-amino-3-carboxypropyl)pseudouridine, 3-(3-amino-3-carboxypropyl) uridine, 3-methylcytidine, 3-methylpseudouridine, 3-methyluridine, 4-demethylwyosine, 4-thiouridine, 5,2′-O-dimethylcytidine, 5,2′-O-dimethyluridine, 5-(carboxyhydroxymethyl)-2′-O-methyluridine methyl ester, 5-(carboxyhydroxymethyl)uridine methyl ester, 5-(isopentenylaminomethyl)-2-thiouridine, 5-(isopentenylaminomethyl)-2′-O-methyluridine, 5-(isopentenylaminomethyl)uridine, 5-aminomethyl-2-geranylthiouridine, 5-aminomethyl-2-selenouridine, 5-aminomethyl-2-thiouridine, 5-aminomethyluridine, 5-carbamoylhydroxymethyluridine, 5-carbamoylmethyl-2-thiouridine, 5-carbamoylmethyl-2′-O-methyluridine, 5-carbamoylmethyluridine, 5-carboxyhydroxymethyluridine, 5-carboxymethyl-2-thiouridine, 5-carboxymethylaminomethyl-2-geranylthiouridine, 5-carboxymethylaminomethyl-2-selenouridine, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyl-2′-O-methyluridine, 5-carboxymethylaminomethyluridine, 5-carboxymethyluridine, 5-cyanomethyluridine, 5-formyl-2′-O-methylcytidine, 5-formylcytidine, 5-hydroxycytidine, 5-hydroxymethylcytidine, 5-hydroxyuridine, 5-methoxycarbonylmethyl-2-thiouridine, 5-methoxycarbonylmethyl-2′-O-methyluridine, 5-methoxycarbonylmethyluridine, 5-methoxyuridine, 5-methyl-2-thiouridine, 5-methylaminomethyl-2-geranylthiouridine, 5-methylaminomethyl-2-selenouridine, 5-methylaminomethyl-2-thiouridine, 5-methylaminomethyluridine, 5-methylcytidine, 5-methyldihydrouridine, 5-methyluridine, 5-taurinomethyl-2-thiouridine, 5-taurinomethyluridine, 5′ (3′-dephospho-CoA), 5′ (3′-dephosphoacetyl-CoA), 5′ (3′-dephosphomalonyl-CoA), 5′ (3′-dephosphosuccinyl-CoA), 5′ diphosphate end, 5′ hydroxyl end, 5′ monophosphate end, 5′ nicotinamide adenine dinucleotide, 5′ triphosphate end, 7-aminocarboxypropyl-demethylwyosine, 7-aminocarboxypropylwyosine, 7-am inocarboxypropylwyosine methyl ester, 7-aminomethyl-7-deazaguanosine, 7-cyano-7-deazaguanosine, 7-methylguanosine, 7-methylguanosine cap (cap 0), 8-methyladenosine, N2,2′-O-dimethylguanosine, N2,7,2′-O-trimethylguanosine, N2,7-dimethylguanosine, N2,7-dimethylguanosine cap (cap DMG), N2,N2,2′-O-trimethylguanosine, N2,N2,7-trimethylguanosine, N2,N2,7-trimethylguanosine cap (cap TMG), N2,N2-dimethylguanosine, N2-methylguanosine, N4,2′-O-dimethylcytidine, N4,N4,2′-O-trimethylcytidine, N4,N4-dimethylcytidine, N4-acetyl-2′-O-methylcytidine, N4-acetylcytidine, N4-methylcytidine, N6,2′-O-dimethyladenosine, N6,N6,2′-O-trimethyladenosine, N6,N6-dimethyladenosine, N6-(cis-hydroxyisopentenyl)adenosine, N6-acetyladenosine, N6-formyladenosine, N6-glycinylcarbamoyladenosine, N6-hydroxymethyladenosine, N6-hydroxynorvalylcarbamoyladenosine, N6-isopentenyladenosine, N6-methyl-N6-threonylcarbamoyladenosine, N6-methyladenosine, N6-threonylcarbamoyladenosine, Qbase, agmatidine, alpha-dimethylmonophosphate cap, alpha-methylmonophosphate cap, archaeosine, cyclic N6-threonylcarbamoyladenosine, dihydrouridine, epoxyqueuosine, galactosyl-queuosine, gamma-methyltriphosphate cap, glutamyl-queuosine, guanosine added to any nucleotide, guanylylated 5′ end (cap G), hydroxy-N6-threonylcarbamoyladenosine, hydroxywybutosine, inosine, isowyosine, mannosyl-queuosine, methylated undermodified hydroxywybutosine, methylwyosine, peroxywybutosine, preQ0base, preQ1base, pseudouridine, queuosine, under modified hydroxywybutosine, uridine 5-oxyacetic acid, uridine 5-oxyacetic acid methyl ester, wybutosine, and wyosine.

Nucleotides can be modified, for example, either synthetically or enzymatically using RNA-modifying enzymes. RNA modifying enzymes include, but are not limited to, methyltransferases, amidinotransferases, transglycosylases, deaminases, dehydratases, isomerases, oxidoreductases, methylphosphate capping enzymes, threonylcarbamoyladenosine synthetases, kinases, thiolases, pseudouridine synthases, guanylyltransferases, triphosphatases, hydrolases, carboxymethyltransferases, acetyltransferases, cysteine desulfurases, selenotransferases, geranyltransferases, dimethylallyltransferases, methyltiotransferases, sulfurtransferases, threonylcarbamoyltransferases, alpha-amino-alpha-carboxypropyltransferases, agmatidine synthases, adenylyltransferases, and thiosulfate sulfurtransferases. For a description of nucleotide modifications and RNA-modifying enzymes, see, e.g., Rozenski et al. (1999). Nucl Acids Res 27: 196-197, Boccaletto et al. (2018) Nucleic Acids Res. 46(D1):D303-D307; MODOMICS database (modomics.genesilico.pl/), the RNA Modification Database (RNAMDB, rna-mdb.cas.albany.edu/RNAmods/), and the RMBase (mirlab.sysu.edu.cn/rmbase).

The RNA template can be derived from a biological sample containing RNA. The biological sample can be any sample of cells, tissue, or fluid isolated from a prokaryotic or eukaryotic organism, including but not limited to, for example, blood, plasma, serum, fecal matter, urine, bone marrow, bile, spinal fluid, lymph fluid, sputum, ascites, bronchial lavage fluid, synovial fluid, samples of the skin, external secretions of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, organs, biopsies, and also samples of cells, including cells from bacteria, archaea, fungi, protists, plants, and animals as well as in vitro cell culture constituents, including but not limited to, conditioned media resulting from the growth of cells and tissues in culture medium, e.g., recombinant cells, and cell components, and also samples containing nucleic acids from viruses.

In certain embodiments, a DNA seed is provided instead of an RNA template, wherein the RNA template for replication is generated by transcription of the DNA seed. In some embodiments, the DNA seed comprises a nucleotide sequence of interest and a 4-way repeat unit. In certain embodiments, the DNA seed is added to the reaction mixture such that the RNA polymerase generates a first RNA comprising the 4-way repeat unit by transcription of the DNA seed. In some embodiments, the method further comprises carrying out a first round of self-templated 3′-extension of the first RNA to produce a second RNA comprising a second 4-way repeat unit; and carrying out a second round of self-templated 3′-extension of the second RNA to produce the RNA template comprising the 4-way repeat configuration.

RNA can be purified before or after replication using methods well-known in the art. For example, RNA may be further purified by immobilization on a solid support, such as silica, RNA adsorbent beads (e.g., oligo(dT) coated beads or beads composed of polystyrene-latex, glass fibers, cellulose or silica), magnetic beads, or by reverse phase, gel filtration, ion-exchange, or affinity chromatography. RNA can also be isolated from suspensions by conventional methods, such as phenol-chloroform extraction or precipitation with alcohol. Alternatively, an electric field-based method can be used to separate the desired RNA molecule from other molecules. Exemplary electric field-based methods include polyacrylamide gel electrophoresis, agarose gel electrophoresis, capillary electrophoresis, pulsed field electrophoresis, and isotachophoresis. See, e.g., RNA: Methods and Protocols (Methods in Molecular Biology, edited by H. Nielsen, Humana Press, 1st edition, 2010); Rio et al. RNA: A Laboratory Manual (Cold Spring Harbor Laboratory Press; 1st edition, 2010); Farrell RNA Methodologies: Laboratory Guide for Isolation and Characterization (Academic Press; 4.sup.th edition, 2009); Zahringer (2012) Lab Times (2-2012):52-63; Garcia-Schwarz et al. (2012) Journal of Visualized Experiments 61:e3890; Rogacs et al. (2012) Anal. Chem. 84(14):5858-5863; Hagan et al. (2009) Anal Chem. 81(13):5249-5256; Righetti (2005) J. Chromatogr. A10 79(1-2):24-40; Gebauer et al. (2011) Electrophoresis 32(1):83-89; herein incorporated by reference in their entireties.

RNA amplified by replication according to the methods described herein can be used for various purposes, including, but not limited to, PCR, ligation, transcriptome analysis, microarray analysis, northern analysis, cDNA library construction, RNA interference, sequencing, vaccines, and directed evolution of RNA aptamers without intermediate conversion to DNA.

Kits

Also provided are kits for amplifying RNA by replication using a transcription polymerase, as described herein. At least one RNA template capable of replication by a transcription polymerase (i.e., RNA comprising a 2-way repeat configuration and a 4-way repeat configuration) may be included in a kit. Kits may also include a transcription polymerase, a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, and optionally modified ribonucleoside triphosphates or analogues. The different components may be contained in separate compositions or in the same composition. In some embodiments, the kit further comprises a container for collecting an RNA sample. The kit may also include reagents for purifying and/or sequencing an RNA sample.

In addition, the kits may further include (in certain embodiments) instructions for practicing the subject methods. These instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit. For example, instructions may be present as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, and the like. Another form of these instructions is a computer readable medium, e.g., diskette, compact disk (CD), flash drive, and the like, on which the information has been recorded. Yet another form of these instructions that may be present is a website address which may be used via the internet to access the information at a removed site.

In certain embodiments, the kit comprises an RNA template comprising a nucleotide sequence selected from Tables 1, 2, or 4, or a sequence displaying at least about 80-100% sequence identity thereto, including any percent identity within this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% sequence identity thereto. In some embodiments, the RNA template comprises (i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat. In some embodiments, the RNA template comprises a G RNA strand comprising two G bases at or close to a 5′ end and two G bases at or close to a 3′ end of the G RNA strand, or a C RNA strand comprising two C bases at or close to a 5′ end and two C bases at or close to a 3′ end of the C RNA strand.

In certain embodiments, the kit further comprises a DNA seed comprising a nucleotide sequence of interest and a 4-way repeat unit.

It will be apparent to one of ordinary skill in the art that various changes and modifications can be made without departing from the spirit or scope of the invention.

EXPERIMENTAL

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.

All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

The present invention has been described in terms of particular embodiments found or proposed by the present inventor to comprise preferred modes for the practice of the invention. It will be appreciated by those of skill in the art that, in light of the present disclosure, numerous modifications and changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention. For example, due to codon redundancy, changes can be made in the underlying DNA sequence without affecting the protein sequence. Moreover, due to biological functional equivalency considerations, changes can be made in protein structure without affecting the biological action in kind or amount. All such modifications are intended to be included within the scope of the appended claims.

Example 1 A Consistent RNA Structural Framework Drives the Origin and Molecular Mechanisms of RNA Replication by a Transcription Polymerase Introduction

To date, five distinct RNA sequences that can be replicated by T7 RNAP have been described, two by Konarska and Sharp (X RNA and Y RNA) (4) and three by Biebricher and Luce (T7rp1, T7rp2 and T7rp3) (5). All five RNAs could form long-hairpin secondary structures. The origins of the RNAs replicated by T7 RNAP have been unclear. Konarska and Sharp speculated that replicating RNA templates could have been pre-existing RNA contaminants in their T7 RNAP preparations, whereas Biebricher and Luce proposed that replicating RNAs form as a result of molecular evolution in T7 RNAP reactions.

By combining next-generation sequencing, microfluidics and bioinformatics with classical biochemistry approaches, we address three questions: (i) How does a DNA-dependent RNA polymerase replicate RNA? We describe subterminal de novo initiation, RNA shape-shifting and interrupted rolling circle synthesis as three underlying mechanisms for RNA replication by T7 RNAP. (ii) How diverse is the family of RNAs that can be replicated by a transcription polymerase? We isolated hundreds of new RNA species replicated by T7 RNAP. (iii) What are the origins of RNAs replicated by a transcription polymerase? Sequence analysis of our large repertoire of RNA species led us to the hypothesis that replicating RNAs can originate through partial instruction from DNA seeds. In support of this hypothesis, we show that T7 RNAP can catalyze the emergence of novel replicating RNAs from a complex DNA seed pool of our own choosing.

Emergence of Diverse but Structurally-Similar Replicating RNAs from No-Template-Added Reactions

We set up a series of T7 RNAP reactions in parallel using aliquots of the same reagents (FIG. 1A). Each reaction contained a high concentration (2 μM) of T7 RNAP. No nucleic acid template was explicitly added to the reactions, with the reaction composition (3) otherwise typical for T7 RNAP. After incubation at 37° C. for ˜24 hours, each reaction contained large amounts of synthesized RNA. The relative gel migration of synthesized RNA products varied from reaction-to-reaction (FIG. 1B), indicating distinct RNAs in each reaction. These data were consistent with the findings of Biebricher and Luce (5).

We analyzed the synthesized sequences for a set of 24 no-template-added T7 RNAP reactions conducted in parallel. Dominant reaction products were sequenced using an RNA-seq protocol that we optimized for efficient reverse transcription of structured RNAs (FIG. 7). Upon unsupervised sequence classification of the reaction products, we observed that each reaction yielded one or more clusters of RNA sequences. Each such cluster—henceforth referred to as an RNA species—was itself a heterogenous population of closely related sequences. For each RNA species, we chose a canonical, abundant sequence that could serve as a “reference” for the information content of the RNA species.

A small number (1 to 3) of RNA species were predominant in each of the 24 sequenced pools (FIG. 1C, Table 1; predominant defined here as relative abundance >5% within a sequenced pool). Reference sequences for the predominant RNA species differed between the 24 no-template reactions (FIG. 1D), although some reactions (e.g. reactions 11 and 22) yielded reference sequences that were related. Furthermore, three of the reference sequences (12.1, 14.1 and 24.1) were related to Y RNA, which was previously characterized as an RNA replicated by T7 RNAP (4).

Most RNA reference sequences were between 60 to 80 bases in length (FIG. 1E), consistent with the migration patterns observed on denaturing gels. As our RNA-seq protocol is strand-specific (e.g. see sequencing of chemically synthesized RNA oligos in FIG. 11), we further analyzed the strand orientations of RNA sequences within each RNA species. Most RNA species showed comparable counts of (i) reads with the same strand orientation as the species reference sequence, and of (ii) reads with a strand orientation complementary to the species reference sequence (FIG. 1F). Of note, RNA replication would be expected to yield sequences of both strand orientations.

Though distinct in sequence content, the RNA species shared structural features (FIG. 1G): (i) A “2-way repeat” configuration characterized by an inverted repeat throughout the RNA length, suggesting possible formation of a long hairpin structure, and (ii) A “4-way repeat” configuration entailing a shorter inverted repeat embedded within each arm of the 2-way repeat. Of interest, the 2-way- and 4-way-repeat configurations were also noted for the previously described RNAs that can be replicated by T7 RNAP (4, 5). The capability of no-template-added, high concentration T7 RNAP reactions to yield novel RNA sequences bearing the 2-way and 4-way repeat patterns was independently reproduced in our study both at Stanford and Galveston.

Our working hypothesis at this point was that the RNA species from no-template reactions can be sustainably replicated by T7 RNAP. To test this hypothesis, we assessed growth of several distinct RNA species in parallel upon dilution into fresh T7 RNAP reactions. A clear sequence correspondence was evident between the RNA species used as spike-in templates in the reactions and the resulting products (FIG. 8), suggesting that the RNAs were replicating. It is to be emphasized that to test templated RNA replication in this experiment (and also in the ensuing work), we used a low reaction concentration of T7 RNAP and checked that no-template-added controls conducted in parallel at the low T7 RNAP concentration did not yield any products detectable by gel electrophoresis. In concordance with previous reports (e.g. 5), we note that T7 RNAP reaction concentration provides a means to experimentally distinguish between (i) RNA replication starting from a defined RNA template (assayed at low T7 RNAP concentration), and (ii) an enzymatic capability to synthesize replicating RNAs unique to a reaction without added template (assayed at high T7 RNAP concentration).

3′ End Sequence Requirements for RNA Replication

Although regeneration of RNA species upon dilution into fresh T7 RNAP reactions suggested an ongoing templated replication process, it remained possible that the RNA species we were analyzing were not themselves templates but rather byproducts of more complex reactions. To establish replication from defined RNA templates, we probed a series of chemically synthesized RNAs for replication by T7 RNAP. In describing the templates tested, we will use the nomenclature of Konarska and Sharp who referred to the complementary strands of replicating RNAs as the G strand and C strand. The G strand sequence has two G bases at the 5′ end and two G bases at the 3′ end, and the C strand, two C bases at the 5′ end and two C bases at the 3′ end. We initially tested replication of chemically synthesized G and C strand sequences for the RNA species 12.1 from FIG. 1 (henceforth, we will refer to this RNA species as Y2 RNA because of its sequence similarity to Y RNA; FIG. 2A). Synthetic Y2 RNA G and C strands failed to instruct efficient RNA synthesis. Mixing the two strands (to assess template activity of the RNA duplex between the G and C strands) did not increase RNA synthesis.

In considering possible features that may define active templates, we initially focused our attention on 3′ end sequences. Compared to the previously proposed replicating RNA 3′ end sequences ( . . . GG-3′ for one strand, . . . CC-3′ for complementary strand) (4, 5), the Y2 RNA species we isolated contained a diversity of 3′ sequence additions ranging from one to a few bases in length. 3′ base additions, a known feature of T7 RNAP activity (e.g. 9, 10), were highly frequent more generally in the RNA species obtained from the no-template, high concentration T7 RNAP reactions (FIG. 9). To mimic the 3′ base additions, we added an extra base to the 3′ ends of the Y2 RNA G and C strands. Upon adding a 3′ extra base either enzymatically (FIG. 2A) or chemically (FIG. 10A), the amounts of T7 RNAP reaction products increased dramatically. These results demonstrate a requirement of 3′ base additions to G and C strand sequences for efficient RNA replication.

We sequenced the RNA products of T7 RNAP reactions from templates with an extra 3′ adenine (FIG. 11). The product sequences corresponded to the input template sequences, as expected for templated RNA replication. Importantly, RNA products of both strand orientations were detected in the same reaction initiated with a particular chemically synthesized RNA template (FIG. 11C). When a T7 RNAP reaction was initiated with the Y2 RNA G strand with an extra 3′ adenine, 35% of the products aligned uniquely to the complementary C strand (FIG. 11A). Furthermore, newly synthesized products with G strand orientation could be identified distinctly from starting template molecules because T7 RNAP adds bases to the 3′ ends of RNA. Indeed, a diversity of 3′ end sequences was observed in the T7 RNAP reaction products that aligned uniquely to the G strand compared to a single 3′ end sequence for the starting template (FIG. 11A). Analogously, newly synthesized RNA molecules of both strand orientations were detected when a T7 RNAP reaction was initiated with the Y2 RNA C strand with an extra 3′ adenine (FIG. 11B).

Our results, in particular the lack of copying of the added 3′ base, inform a “subterminal de novo initiation” model for RNA replication by T7 RNAP (FIG. 2B). Under our model, T7 RNAP de novo initiates upstream of the 3′ extra bases rather than at the 3′ end. After 5′->3′ copying of the RNA template, T7 RNAP adds 3′ extra bases to the RNA product. In effect, the 3′ base addition confers the appropriate 3′ end for the RNA product to subsequently serve as an efficient template, while maintaining the chain length of the replicating RNA species.

The requirement of 3′ extra bases exemplifies a hallmark of RNA replication that is shared between numerous viral RNA-dependent RNA polymerase (RdRp) systems (11) and the transcription polymerase studied here. A possible mechanism for the function of 3′ extra bases is suggested by experiments with the RdRp of bacteriophage Qβ showing that a 3′ extra base can provide stabilizing interactions at the polymerase active site for more efficient de novo initiation (12).

Replicating RNAs as Sequence Ensembles

Viral replicating RNAs are heterogeneous populations consisting of multiple replication-competent sequences (e.g. 13). We assessed the population-level sequence heterogeneity of RNAs replicated by T7 RNAP. Upon examining full-length sequences from replicating RNA populations, we found that sequence variants on the two RNA strands were complementary and that complementary variants occurred at similar frequencies (FIG. 3). As an example of such complementarity, for the RNA species shown in FIG. 3B, G->A variation at position 44 (from the 5′ end) on one strand occurs at a frequency of ˜1.1%, while C->U variation at position 21 (from the 5′ end) on the complementary strand (this is position 44 from the 3′ end) occurs at a frequency of ˜1.3%. As our RNA-seq protocol is strand-specific (e.g. see sequencing of chemically synthesized RNA oligos in FIG. 11), complementary variation on the two strands shows that RNA templates bearing sequence variants can be replicated. RNA species replicated by T7 RNAP thus consist of multiple replication-competent sequences, and should be conceptualized as sequence ensembles rather than as individual sequences.

Structural Requirements for RNA Replication

2-way and 4-way repeats were structural features shared by the RNA sequences obtained from the no-template-added, high concentration T7 RNAP reactions. We performed high-throughput mutagenesis of the 2-way and 4-way repeats to directly test whether these particular structural features are required for RNA replication. Specifically, we designed a series of degenerate libraries; each library was made by randomizing a subset of base identities at a distinct set of 5 or 6 positions in either X RNA (4) or Y2 RNA. Each library thus contained 4⁵-4⁶ RNA sequence variants. To test the 4-way repeat requirement, four potentially base pairing positions in the 4-way repeat were randomized. To test the 2-way repeat requirement, two potentially base pairing positions in the 2-way repeat (but outside the 4-way repeat) were randomized. We performed T7 RNAP replication reactions with the degenerate libraries to enrich for efficiently replicating RNAs, sequenced RNA populations before and after replication, and asked whether the replicated populations showed sequence co-constraints between the positions with randomized bases (FIG. 4).

At the positions used to test the 2-way repeat requirement, the combinations represented after RNA replication were dominated by Watson-Crick base-pairs (FIG. 4A). At the positions used to test the 4-way repeat requirement, the most abundant RNA sequences had one of the four possible 4-way Watson-Crick base combinations—(A,U,A,U), (U,A,U,A), (G,C,G,C) or (C,G,C,G) (FIG. 4B).

It should be noted that not all Watson-Crick base combinations were replicated efficiently for any given degenerate library. But for each set of positions used to test the 2-way or 4-way repeat requirements, we did detect at least two abundant Watson-Crick base combinations (FIGS. 4A and 4B).

We also constructed a degenerate library where we randomized the base identities at only two of the four potentially base pairing positions in a 4-way repeat. After templated replication of this library, the most abundant RNA sequences contained a single 4-way Watson-Crick base combination that was expected given the identity of the fixed bases in the 4-way repeat (FIG. 4C). We conclude that both the 2-way and 4-way repeats are required for efficient replication of X and Y2 RNA by T7 RNAP.

Based on the function of the 2-way repeat, we suggest that a long hairpin structure is required for RNA replication by T7 RNAP. A long hairpin may thermodynamically allow for strand separation of the complementary strands, which would be needed to generate active single-stranded templates for continued replication (14).

The functional role of the 4-way repeat suggests that the capability to change secondary structure (“shape-shift”) is required for an RNA template to be efficiently replicated by T7 RNAP (FIG. 4D). Possible advantages conferred by shape-shifting include faster strand separation of the complementary strands (15) and more efficient unwinding of the RNA template by T7 RNAP.

Interrupted Rolling Circle Mechanism for RNA Concatemer Synthesis

RNA concatemers—RNA chains consisting of multiple, full-length repeats of template sequence—have been identified as intermediates during replication of viroids and Hepatitis delta (16, 17). A ladder of RNA concatemers (dimers, trimers, tetramers etc.) also forms during RNA replication by T7 RNAP (3). To investigate mechanisms of RNA concatemer formation, we analyzed the sequences of RNA dimers obtained from T7 RNAP reactions starting with diverse pools of chemically synthesized RNA monomer templates. For terminology, we define an “RNA monomer” as comprising a single repeat of full-length template RNA sequence and an “RNA dimer” as comprising two repeats.

We considered two types of mechanisms for RNA dimer formation using monomer templates (FIG. 5A)—1) Uni-templated and 2) Bi-templated. In a uni-templated mechanism, the same monomer template molecule instructs synthesis twice to form the dimer. In a bi-templated mechanism, two different monomer template molecules (which may still have the same sequence) instruct synthesis of each half of the dimer.

The presence of a diversity of monomer templates in the same T7 RNAP reaction was a key aspect of the experimental design to elucidate the RNA dimer formation mechanism (FIG. 5B) (18). We sequenced RNA dimers from two starting monomer template pools called X₁ and Y2₁ (these pools were also used earlier for FIG. 4 experiments, and were constructed by randomizing a subset of base identities at six positions each in the X RNA and Y2 RNA sequences, respectively). We expected that uni-templated synthesis would result in the two halves of RNA dimers containing the same six base combination at the positions with initially randomized bases. In contrast, bi-templated synthesis would be expected to lead to relatively rare agreement of the six base combination between the two dimer halves (in proportion to the concentration of the six base combination in the reaction pool).

We found strong sequence agreement between the six base combinations of both dimer halves for the vast majority of dimer sequences (analysis in bulk in FIG. 5C and by individual RNA templates in FIG. 5D). These results suggest that uni-templated synthesis is the dominant mechanism for formation of RNA dimers. As predicted by a uni-templated synthesis mechanism, we also found that sequence variants located outside the intentionally randomized six bases were concordant between the dimer halves (FIG. 13). Of note, the concordance of sequence variants between RNA dimer halves provides direct and independent evidence for active replication of RNA templates bearing sequence variation compared to the reference sequence (shown earlier in FIG. 3).

How does T7 RNAP use the same template molecule processively to instruct multiple rounds of RNA synthesis? We propose that after reaching the 5′ end of a replicating RNA template during RNA synthesis, T7 RNAP can jump (19) from the 5′ end to the 3′ end of the template without dissociation of the RNAP-template-product complex. Continued RNA synthesis after the jump appends a new copy of the template to the existing RNA product. We refer to this mechanism as interrupted rolling circle synthesis (FIG. 5E).

We further examined the junction sequences between the two RNA dimer halves to assess whether the proposed jumping of T7 RNAP is associated with any sequence signatures. A diversity of sequences was found at the dimer junction. The junction sequences qualitatively resemble the 3′ end sequences of RNA monomers (including the extra base additions) followed by the 5′ end sequences of RNA monomers. Further, as would be expected for RNA dimer synthesis from a linear monomer template, the junction sequence for a particular dimer molecule did not necessarily agree with the 3′ end sequence of that dimer (FIG. 14). Two other pieces of evidence also suggest that the monomer templates instructing dimer synthesis were linear rather than circular: (i) we obtained RNA dimers starting with monomer RNAs bearing ends (5′-OH and 3′-OH) that are chemically incompatible for ligation, and (ii) Konarska and Sharp found that explicitly circularized X or Y RNA were not replicated efficiently (4).

Potential Relevance of an Interrupted Rolling Circle Model for Viroids and Hepatitis Delta

Current mechanistic models for replication of viroids and Hepatitis delta involve RNA concatemer intermediates produced by rolling circle synthesis using circular RNA templates. Linear RNA molecules are also detected alongside circular RNAs in populations of viroids and Hepatitis delta. It has been proposed that the linear RNA molecules may be active as templates for instructing RNA synthesis (20, 21 and references therein) but how linear RNAs could template synthesis of RNA concatemers remained unanswered.

An interrupted rolling circle mechanism with linear RNA templates offers a plausible alternative to the use of circular templates for RNA concatemer synthesis. To assess the applicability of an interrupted rolling circle mechanism to viroid replication, we examined published data for avocado sunblotch viroid (ASBVd) (22) and peach latent mosaic viroid (PLMVd) (20). Both ASBVd and PLMVd belong to the Avsunviroidae family of viroids, and are replicated in the chloroplasts of infected plants. Interestingly, ASBVd may be replicated by a chloroplastic RNA polymerase similar to T7 RNAP (8). ASBVd and PLMVd populations contain particular 5′ triphosphate-bearing, monomer-length, linear RNA sequences for both strand orientations. The following two aspects of these linear monomers are more parsimoniously explained by a linear template model rather than a circular template model: (i) Initiation of RNA synthesis (or 5′ end specification): The measured 5′ initiation sites for ASBVd and PLMVd are such that the 5′ initiation site for the (+) strand corresponds to the 3′ end of a linear (−) molecule present in the RNA population and the 5′ initiation site for the (−) strand corresponds to the 3′ end of a linear (+) molecule in the population. Under a circular template model, such positioning for the 5′ ends of the (+) and (−) strands would be a priori considered coincidental, with an additional source of specificity such as particular structural or sequence motifs (20, 22) required to explain the initiation site positioning. Under a linear template model, the measured 5′ ends of the (+) and (−) strands would be expected simply based on full-length copying. (ii) Termination of RNA synthesis (or 3′ end specification): The presence of a defined set of monomer-length linear molecules in ASBVd and PLMVd populations requires an explanation for precise 3′ end generation. Under a circular template model, the RNA 3′ ends can be explained by positing specific termination signals for RNA synthesis or by particular RNA cleavage events in vivo. Under a linear template model, the RNA 3′ ends can be explained more simply by the termination of RNA synthesis upon reaching the template end.

An implication of the linear template model may be that viroids and Hepatitis delta circularize not for their replication but to withstand other selective pressures such as degradation by exonucleases.

Origin of Replicating RNAs Via Molecular Evolution

The variability observed in the sequences of replicating RNAs between no-template-added reactions raises several fundamental questions regarding the origins of replicating RNAs. Do distinct replicating RNAs originate in each reaction or are pre-existing replicating RNAs amplified? If new replicating RNAs do originate in each reaction, are they assembled from single nucleotides or is their formation partly templated?

We conjectured that obtaining many additional sequences of replicating RNA species may provide insights towards these questions of replicating RNA origins. We thus developed a microfluidic assay to conduct no-template reactions in high-throughput (FIG. 15). By splitting our usual 10 μl reaction volume into ˜170 thousand isolated drop reactions (each drop was ˜60 picoliters), we expected to capture a higher diversity of replicating RNAs that would otherwise be lost because of competition in bulk. We analyzed the RNA contents of the no-template, high concentration T7 RNAP reactions in drop format by aggregating ˜10⁵ drops at a time, and found, as expected, numerous RNA species (Table 2) that had different sequences but similar structures to what was observed in the earlier tube reactions. Examples of RNA species obtained from the aggregated drop reactions are shown in FIG. 6E, FIG. 18 and FIG. 20B.

Within the large repertoire of RNA species we compiled using drop reactions, a subset of the RNAs contained sequence stretches that matched perfectly to known biological sources. Matches were commonly found to humans and to biological materials or organisms found in proximity to humans. From one no-template-added drops experiment, where we had included bovine serum albumin (BSA) in our reactions to aid drop-reaction generation, we isolated RNA sequences similar to a replicating RNA sequence T7rp1 reported previously by Biebricher and Luce (5). Interestingly, T7rp1 (and also the RNA sequences we isolated) strongly matched a sequence found in the genomes of cow and yak (FIG. 19). These results suggested that replicating RNAs could evolve from residual nucleic acids present in the high concentration T7 RNAP reactions. Of note, we never synthesized or handled any of the replicating RNA sequences reported by Biebricher and Luce.

As with drop reactions, we also found novel RNA species that matched known genomes upon sequencing more no-template-added reactions set up in tubes (e.g. FIG. 6A shows an RNA species matching humans and FIG. 20A shows an RNA species matching a bacterium commonly found in cheese (23)).

A working hypothesis at this point was that the RNAs replicated by T7 RNAP can originate through partial instruction from DNA seeds. We first focused on DNA seeds as a possibility (rather than the alternate possibility of RNA seeds) because the detected matches in replicating RNAs were represented throughout the genome rather than in specific transcribed regions.

To experimentally test the hypothesis that replicating RNAs can originate from DNA seeds, we assessed whether T7 RNAP could catalyze the emergence of new replicating RNAs from a complex DNA seed pool of our own choosing (FIG. 6B). The seed pool we used was a mixture of well-characterized model system genomes [three nematode species (Caenorhabditis elegans, Caenorhabditis remanei and Caenorhabditis brenneri), yeast (Saccharomyces cerevisiae strain S288C), coliphage lambda and a laboratory plasmid]. We chose these particular sources of DNA to reflect a range of genome sizes and sequence complexities. An additional consideration was that the chosen DNA sources did not significantly match any of the replicating RNAs that we had previously isolated. With the exception of lambda DNA which was isolated from purified phage, the DNA seeds were derived from cellular sources. Hence, we extensively treated the DNA seeds with RNase A and RNase I before use. After treating with RNases and combining the DNA seeds from all the chosen sources, we split the seed pool into three equal parts. One part underwent no further treatment, the second part was treated with DNase and the third part was heated with alkali (0.2 N sodium hydroxide at 70° C. for 1 hour) to further hydrolyze any possible remaining RNA (hot alkali treatment also provided an assessment of seed activity from denatured DNA).

We conducted high concentration T7 RNAP reactions in drop and tube format for four experimental conditions in parallel: (1) Unseeded, (2) Seeded with DNA pool (which we had prepared), (3) Seeded with DNase-treated DNA pool, and (4) Seeded with hot alkali-treated DNA pool. For each experimental condition, we sequenced aggregated drop and tube reactions. From comparable reaction volumes and sequencing depths, the number of replicating RNAs identified per reaction was 53+/−22 (mean+/−standard deviation) for 8 aggregated drop reactions and 7+/−5 for 6 tube reactions (Table 2). We then used BLAST (24) to align the replicating RNAs obtained from all four conditions to the expected sequences present in our designed DNA pool. As a control, we also aligned the replicating RNAs to the complete genomes of all other species that were available in the RefSeq Genomic database (25). Of the four experimental conditions examined, only the “Seeded with DNA pool” and “Seeded with hot alkali-treated DNA pool” conditions yielded replicating RNAs that were derived from our designed DNA pool (FIGS. 6C, 6E, 20B). Significant matches specific to our DNA pool were absent in two negative controls—the “Unseeded” and “Seeded with DNase-treated DNA pool” conditions (FIG. 6C). These results demonstrate that the RNAs replicated by T7 RNAP can originate from DNA seeds.

What may be the molecular mechanism for the origin of replicating RNAs from DNA seeds? A striking pattern is revealed when the location of the matching seed in a replicating RNA sequence is compared to the positions of the 4-way repeat units for that sequence. The seed match starts at an end of the replicating RNA and extends up to the second 4-way repeat unit that is encountered from the start of the match (FIG. 6D). These data are consistent with models for the formation of replicating RNAs which at minimum include the steps of (FIG. 6F): (i) T7 RNAP-catalyzed transcription of a DNA seed to RNA, (ii) One round of self-templated 3′ extension of RNA to acquire a second 4-way repeat unit, and (iii) A second round of self-templated 3′ extension of RNA to acquire the full 2-way and 4-way repeat configurations (26, 27). This minimal series of biochemical steps can lead to the formation of RNA molecules with 2-way and 4-way repeat configurations. Once such RNAs are formed, they have the potential to replicate efficiently (based on FIG. 4) and to become predominant in the high concentration T7 RNAP reactions because of Darwinian selection. Thus, an RNA structural framework drives the DNA-seeded emergence of replicating RNAs.

In terms of biological significance, our work provides an experimental window into how replicating RNAs such as viroids or Hepatitis delta might originate via host transcription polymerase activities. Just as new replicating RNAs originate from distinct DNA seeds in our T7 RNAP reactions, so may emergence of new RNA replicons be ongoing in nature, independent of other pre-existing RNA replicons. Of note, derivation from host nucleic acids is one of several hypotheses that have been put forth for the origins of viroids and Hepatitis delta (28-30).

Our work also provides new insights into the rich history of mysterious products emerging from in vitro no-template-added reactions for both DNA and RNA polymerases (e.g. 31, 32). A key question was whether such reactions evidence molecular evolution or are the observed products a result of amplification of pre-existing templates. Ascertaining the involvement of a pre-existing template was challenging because a replicative cycle triggered by a single template molecule (which would be below detection limits) could have resulted in the observed products. Emergence of novel RNA replicons from a complex DNA seed pool of our own choosing (FIG. 6B-E) shows that high concentration T7 RNAP reactions can witness DNA-seeded origin and evolution of replicating RNAs rather than just amplification of pre-existing templates.

Biotechnological Applications

We have shown that the sequence space of RNA templates that can be replicated by T7 RNAP is large. T7 RNAP-catalyzed RNA replication can thus serve as a valuable strategy for a myriad in vitro RNA amplification applications, including direct selection of RNA aptamers without intermediate conversion to DNA and synthesis of large amounts of RNA. In vivo applications of T7 RNAP-RNA replication may rely on transfection of cells with pools of replicating RNAs synthesized in vitro or on stable maintenance of replicating RNAs in vivo. The latter approach is facilitated by the relative simplicity of T7 RNAP as a single polypeptide chain that has already been transgenically expressed in vivo in a variety of organisms. RNAs replicated by T7 RNAP consist of long 2-way repeats and hence, may be particularly suitable for gene silencing applications utilizing hairpin RNAs.

Role of 3′ Base Additions in RNA Replication

To distinguish between subterminal (FIG. 2B) and terminal initiation mechanisms, we analyzed the 5′ and 3′ sequence ends of RNA products from reactions initiated with templates bearing an extra 3′ adenine. Under a terminal initiation model for such templates, uracil would be expected as the 5′ base for complementary strand products. Further, for products with the same strand orientation as the starting template, an expectation with terminal initiation would be that a 3′ consensus adenine is positioned in the sequences before the occurrence of diverse, T7 RNAP-catalyzed, 3′ base additions. On the other hand, under a subterminal initiation model, both (i) 5′ uracil for the complementary strand products and (ii) a 3′ consensus adenine for the same strand products, would not be expected.

In our data, complementary strand products do not evidence 5′ uracil above background levels (background measured using control chemically synthesized RNA oligos; a background of 5′ extensions was expected from reverse transcriptase activity during RNA-seq library preparation) (FIG. 10C). An interpretation of our observed 5′ sequence distributions is that guanine serves as the main 5′ initiation nucleotide on one strand and cytosine on the other strand, consistent with the 5′ initiation nucleotide identities experimentally determined by Konarska and Sharp using two different assays (3). Furthermore, in our data, same strand products did not contain a 3′ consensus adenine (FIG. 11). 3′ base additions by T7 RNAP were not positioned after a possible 3′ consensus adenine; instead, diverse 3′ base additions were detected prior to the expected position of a 3′ consensus adenine. Thus, analysis of both the 5′ and 3′ sequence ends of RNA products supports a subterminal initiation model over terminal initiation.

We note that previously published chromatography data are consistent with our findings regarding the significance of 3′ base additions in RNA replication by T7 RNAP. The high frequency of 3′ base additions in replicating RNA populations may explain why Konarska and Sharp observed all four bases at the 3′ end of X RNA using a radioactivity-based assay (FIG. 7D in (4)). Furthermore, a role of 3′ extra bases could potentially have been masked in previous studies on T7 RNAP-RNA replication because the RNA templates were prepared using run-off transcription of synthetic DNA oligos, which is known to result in RNA products with 3′ extra bases (e.g. 9, 10).

We further note a slight gel mobility difference between Y2 RNA replication products and chemically synthesized Y2 RNA oligos (FIG. 2A, FIG. 10A) on our denaturing gels [10% TBE-urea gel (29:1 acrylamide/bis)]. The mobility difference may be collectively accounted for by (i) the different 5′ chemical ends of replication products (5′-triphosphate) and RNA oligos (5′-hydroxyl) (FIG. 10B), and (ii) 3′ base additions longer than one nucleotide in replication products.

Requirement of 2-Way and 4-Way Repeats for Efficient RNA Replication

2-way and 4-way repeats confer a fitness advantage for RNA replication by T7 RNAP. However, RNA templates with distortive mutations that would disrupt perfect complementarity in the 2-way or 4-way repeats can (at least in some cases) still be replicated, as evidenced by (i) strong correlation between frequencies of distortive mutations on one strand and frequencies of their complementary mutations on the other strand (FIG. 3), and (ii) concordance of distortive mutations between the two halves of RNA dimers (FIG. 13). The capability of templates with distortive mutations to be replicated shows a lack of rigid RNA structure requirements for replication, and has implications for replicating RNA evolution: RNAs could evolve gradually through single sequence changes at a time.

Additionally, we note that for the Y21 degenerate library in FIG. 4, the second most abundant 4 base combination was not Watson-Crick but was a single sequence change away from the most abundant 4 base combination (which was a 4-way Watson-Crick base combination). The specific single sequence change in the second most abundant 4 base combination would not allow a Watson-Crick base pair but could still allow a GU wobble base pair for one of the replicating RNA strands.

Interrupted Rolling Circle Mechanism for RNA Concatemer Synthesis

We performed several quantitative analyses to assess the sequence agreement between RNA dimer halves. We found that the observed sequence agreement between dimer halves was much more frequent than would be expected based on a bi-templated synthesis model (FIG. 12). These results suggest that uni-templated synthesis is the dominant mechanism for formation of RNA dimers.

We had obtained RNA dimers starting with mixtures of monomer templates containing intentionally randomized bases at specific positions. In evaluating sequence variants located outside the intentionally randomized bases in RNA dimers, we found that the concordance of variants between the two dimer halves was more frequent by 4.5-7 fold than would be expected based on the variants occurring independently in each dimer half (FIG. 13). To give a sense of the magnitude of this concordance: for most sequence variants, concurrent incidence in both dimer halves was more frequent than incidence in either half alone. These results again support a uni-templated synthesis mechanism for RNA dimer formation.

From examining previously published data on the RNA concatemers of X RNA (3), we note that the interrupted rolling circle model quantitatively explains the RNase T1 cleavage patterns observed for these RNA concatemers. A previous report had hypothesized an apparent rolling-circle mechanism operating on single-stranded linear DNA oligos transcribed by T7 RNAP (33). But in that report, only a single template sequence was used per reaction and therefore, the data shown were also consistent with a mechanism for RNA concatemer formation involving multiple template molecules.

A structural interpretation of our interrupted rolling circle model may be that upon completion of a round of template copying, the 5′ and 3′ ends of a replicating RNA monomer template are close to each other in space at the active site of T7 RNAP. The proximity of the template ends in space may facilitate jumping of T7 RNAP from the 5′ to 3′ end.

The mechanism generating the extra bases observed at the junction between the two halves in RNA dimers is not fully known. The extra bases at dimer junctions could be a result of 3′ extra base additions to RNA products by T7 RNAP as it jumps from the 5′ to 3′ end of the RNA template and/or a result of the copying of the extra bases present at the 3′ end of the monomer template.

Origin of Replicating RNAs Through Partial Instruction from DNA Seeds

Before conducting the no-template-added, high concentration T7 RNAP reactions in drop format, we first tested whether our microfluidic assay could support replication of our characterized chemically synthesized RNA templates at low concentrations of T7 RNAP. Templated RNA replication catalyzed by T7 RNAP in drops was evident using (i) gel electrophoresis analysis, whereby RNA synthesized cumulatively in a pool of drops could be visualized, and using (ii) a fluorescence imaging-based drop-by-drop assay of RNA synthesis, with inclusion of a nucleic-acid binding dye into the drops. In the latter approach, dilution of the starting RNA template allowed us to track the percentage of drops that were fluorescent after reaction incubation as a function of the starting RNA template concentration, akin to digital droplet PCR (FIG. 17).

For the RNAs synthesized in no-template-added, high concentration T7 RNAP drop reactions, we also conducted functional tests to assess replication-competence. Specifically, aggregated drop reactions were used in bulk as templates in fresh, microliter-scale, low concentration T7 RNAP reactions and the resulting RNA pools sequenced. The numerous RNA species from the initial no-template-added drop reactions that were amplified in the bulk, low concentration T7 RNAP reactions exhibited typical sequence and structural hallmarks of replicating RNAs (FIG. 18)—(i) 2-way repeats, (ii) 4-way repeats and (iii) GG and CC end sequences outside the 2-way repeats: one strand containing two G bases at or close to both the 5′ and 3′ ends (and therefore, the complementary strand containing two C bases at or close to both the 5′ and 3′ ends). We concluded that novel replicating RNAs can be isolated from no-template-added drop reactions.

Of note, no-template-added tube and no-template-added aggregated drop reactions migrated differently on denaturing gels. The tube reactions appeared mostly as well-defined bands corresponding to particular replicating RNA species (e.g. FIG. 1B). The aggregated drop reactions appeared as smears (FIG. 16), reflecting the rich diversity of RNA products that was also evident upon high-throughput sequencing.

We performed the analyses presented in FIG. 6B-E and FIG. 20B as follows. For each sequenced pool from an aggregated drop reaction or tube reaction, we performed a global, sequence-agnostic analysis and grouped all the detected sequences into RNA species. For each of the aggregated drop reactions, a subset of species contained complementary RNA sequences with GG and CC end sequences located outside a 2-way repeat configuration. Within this subset of RNA species, two distinguishable clusters of species were observed, corresponding to species with long and short 2-way repeats. Based on previous experimental results (FIGS. 1, 4, and 18), we identified as replicating RNAs from all drop and tube reactions, RNA species that contained two sequence hallmarks: (i) long 2-way repeats, and (ii) GG and CC end sequences outside the 2-way repeats (with the molecules containing the GG and CC end sequences being complementary). These two sequence hallmarks were also found to be sufficient to identify the predominant RNA species in cases where the reaction products migrated as well-defined bands on denaturing gels (i.e. tube reactions that had been set up in parallel as part of the experiment). It should be noted that other RNA species in the aggregated drop reactions that we are currently excluding from analysis (e.g. species with short 2-way repeats or species without the GG and CC end sequences) could also be competent for replication. Our current knowledge of replicating RNA sequence features stems primarily from tube-based replication assays which are inherently competitive in nature. Compartmentalizing the volume of a tube reaction into smaller drop reactions could lead to better detection of replicating RNA species with divergent sequence features.

The chemical space of nucleic acids that can seed emergence of novel RNA replicons is not fully known. Although our experiments evidence the origin of replicating RNAs from DNA seeds, it is foreseeable that particular RNA molecules could also work as seeds in certain circumstances (34). For example, we might expect any RNA that mimics an intermediate product involved in the proposed model in FIG. 6F to serve as a seed. Furthermore, our assays do not currently allow us to gauge relative seeding efficiencies for different types of DNA molecules (single-stranded versus double-stranded, or with differing seed length, sequence identity or end configuration such as 3′ overhang versus 5′ overhang versus blunt ended for dsDNA seeds). As we obtained replicating RNAs matching our complex seed pool both before and after treatment of the seed pool with hot alkali, both single-stranded and double-stranded DNA molecules may be competent as seeds.

It is important to appreciate the difference between (i) a replicating RNA originating from a seed and (ii) being able to detect a replicating RNA as having originated from a seed. We can only confidently assign replicating RNAs to initiating seeds when the detected seed matches are long, and essentially mismatch- and gap-free. Such high-quality seed matches were observed for only a subset of replicating RNAs. The lack of a significant seed match to a replicating RNA could be for several reasons, including: (i) the initial seed used in generating the replicating RNA may have contributed only a short sequence, (ii) the replicating RNA may have diverged in sequence from its seed due to extensive mutation and selection, (iii) the seed sequence may be absent from our current databases, and (iv) the replicating RNA could conceivably have originated through alternative mechanisms such as de novo assembly from single nucleotides (31).

Some details of the mechanistic scheme proposed in FIG. 6F are also worth clarifying: (i) The RNA product in the first step of the model (“Transcription”) contains a sequence stretch matching the DNA seed (red box in FIG. 6F) but may additionally contain novel 5′ and 3′ end sequences generated by T7 RNAP (black stubs flanking the red box); (ii) The first round of RNA-templated 3′ extension may be primed by bases that were copied from the DNA seed and/or by extra bases added by T7 RNAP to the 3′ end of the transcribed RNA product; (iii) While the two rounds of RNA-templated 3′ extension are depicted as being intramolecular in FIG. 6F, the possibility of RNA-templated intermolecular 3′ extension cannot be excluded; (iv) More than two rounds of RNA-templated 3′ extension could also occur [e.g. sequence in the loop region of the putative long hairpin could (at least in some cases) be derived from an additional round of RNA-templated 3′ extension]; and (v) RNA-templated synthesis of new RNA chains could occur at several intermediate steps before the formation of a full-length replicating RNA.

RNA Replication by the DNA-Dependent RNA Polymerase of Bacteriophage T3

We found that T3 RNA polymerase can replicate an RNA species with a reference sequence similar to Y2 RNA. The capability of T3 RNA polymerase to replicate RNA was also noted by Biebricher and Luce (5).

Materials and Methods Key Reagents/Equipment

-   -   10% TBE-Urea gels (Bio-Rad #4566033)     -   TBE running buffer (prepared from National Diagnostics #EC-860)     -   Gel Loading Buffer II (Ambion #AM8547) (solution of 95%         Formamide, 18 mM EDTA,     -   0.025% SDS, Xylene Cyanol and Bromophenol Blue)     -   SYBR Gold 10,000× Concentrate (ThermoFisher #511494)     -   Nucleoside triphosphates or NTPs (NEB #N0466)     -   PEG 8000 (Fluka #81268)     -   0.2 micron syringe filter (Pall Life Sciences #4192)     -   DTT (Gold Biotechnology #DTT10)     -   Spermidine (Sigma #S0266)     -   0.1% (v/v) Triton X-100 (Sigma #T8787)     -   1.5 ml siliconized tubes (Thomas Scientific #2591L12)     -   Glycoblue (Ambion #AM9515)     -   T4 RNA ligase 2, truncated, K227Q (NEB #M0351)—50% PEG 8000 and         10×T4 RNA ligase buffer (500 mM Tris-HCl, 100 mM MgCl₂, 10 mM         DTT, pH 7.5 at 25° C.) supplied with this product are used in         the 3′ adapter ligation reactions     -   SuperScript III (Invitrogen #18080044)—5× First Strand Buffer         (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl₂) and 0.1 M         DTT supplied with this product are used in the reverse         transcription reactions     -   RNase OUT (Invitrogen #10777019)     -   Deoxynucleoside triphosphates dNTPs (Sigma/Roche #11969064001)     -   CircLigase II (Epicenter #CL9025K)—10× circLigase II buffer         (0.33 M Tris-acetate (pH 7.5),     -   0.66 M potassium acetate and 5 mM DTT), 50 mM MnCl2 and 5M         Betaine supplied with this product are used in cDNA         circularization reactions     -   CircLigase (Epicenter #CL4115K)—10× circLigase buffer (0.5 M         MOPS (pH 7.5), 0.1 M KCl, 50 mM MgCl₂, and 10 mM DTT), 50 mM         MnCl₂, 5M Betaine and 1 mM ATP supplied with this product are         used in cDNA circularization reactions TrackIt 10 bp DNA ladder         (Invitrogen #10488019)     -   20/100 ladder (IDT #51-05-15-02)     -   2× Phusion Master Mix (Thermo Fisher #F531)     -   HFE-7500 containing 2% wt/wt 008-FluoroSurfactant (RAN         Biotechnologies #008-FluoroSurfactant-2wtH-50G)     -   TURBO DNase and 10× TURBO DNase buffer from TURBO-DNase kit         (Ambion #AM1907)     -   ¹H,¹H,²H,²H-Perfluoro-1-octanol (PFO) (Sigma #370533)     -   Adenosine 3′, 5′-diphosphate disodium salt (pAp) (Carbosynth         #NA15774)     -   T4 RNA ligase 1 (NEB #M0204S)—10×T4 RNA ligase reaction buffer         (500 mM Tris-HCl, 100 mM MgCl₂, 10 mM DTT, pH 7.5 at 25° C.)         supplied with this product is used for 3′ base addition         reactions     -   Lambda phage DNA (NEB #N3011S)     -   S. cerevisiae genomic DNA (Sigma/EMD Millipore #69240)     -   C. elegans strain PD1074 (a wild-type N2 strain characterized         extensively in the Fire lab)     -   C. remanei strain PB4641, gift from Marie-Anne Felix and         Aurélien Richaud     -   C. brenneri strain JU1397, gift from Marie-Anne Felix and         Aurélien Richaud     -   RNase A (ThermoFisher #EN0531)     -   RNase I (Ambion #AM2295)     -   Zymo Clean and Concentrator kit (Zymo Research #D4014)     -   ZymoPURE Plasmid Miniprep kit (Zymo Research #D4208S)     -   Restriction enzyme MnII (NEB #R0163S), supplied with 10×         CutSmart buffer (500 mM Potassium Acetate, 200 mM Tris-acetate,         100 mM Magnesium Acetate, 1 mg/ml BSA, pH 7.9 at 25° C.)     -   Restriction enzyme Hpy188III (NEB #R0622S), supplied with 10×         CutSmart buffer MS2 genomic RNA (Sigma/Roche #10165948001) used         for creating an internal, spike-in standard for quantification         of RNA-Seq libraries     -   Qubit dsDNA BR (ThermoFisher #Q32850) and HS (ThermoFisher         #Q32851) kits for quantification of dsDNA

DNA and RNA Oligonucleotide Synthesis

Oligos were purchased from IDT, and are listed in Table 3.

Polyacrylamide Gels

Samples were loaded on denaturing gels after adding an equal volume of Gel Loading

Buffer II and denaturing at 95° C. for >=2 minutes. Gels were pre-run for at least 30 minutes before sample loading. Gels were stained in a 1:5000-1:10,000 dilution of SYBR Gold stock reagent (dilution in 1×TBE) for 15-30 minutes covered with aluminum foil on a rocker. Gels were imaged using an Alphalmager HP system (ProteinSimple). Two 10 base ladders were used as markers on denaturing gels: (i) TrackIt 10 bp DNA ladder and (ii) 20/100 ladder mixed with a set of DNA ultramers to get a 10 base ladder from 20-200 bases. The ladders were also dissolved in Gel Loading Buffer II and denatured at 95° C. prior to gel loading.

For display purposes, for each of the gel images shown in FIG. 1, FIG. 8, FIG. 10 and FIG. 16, a constant gamma correction (γ=0.3) was applied uniformly across the entire image using MATLAB (Natick, Mass.). For display purposes in FIG. 2A, a constant gamma correction (γ=0.3) and a constant increase in brightness were applied uniformly across the entire set of gel images using MATLAB. For display purposes in FIG. 7, a constant gamma correction with γ=3.33 was applied uniformly to the denaturing gel images (first three gels from left to right) and with γ=1.0 was applied uniformly to the PCR gel image (rightmost gel) using AlphaView software (ProteinSimple). Gel images that are shown for side-by-side comparison (FIG. 2A, FIG. 8 and FIG. 10A) were all taken at the same exposure.

T7 RNAP-RNA Replication Reactions

High concentration T7 RNAP was either prepared in-house using a protocol previously used to purify crystallography-grade T7 RNAP (35), or purchased as a special order from New England Biolabs (NEB). High concentration T7 RNAP was stored at −80° C. Commercially available low concentration T7 RNAP preps (from either NEB or Agilent) were stored either at −20° C. or −80° C. Unless otherwise stated, buffer composition of T7 RNAP reactions was: 40 mM Tris-HCl (pH 8), 80 mg/ml PEG 8000, 20 mM MgCl₂, 5 mM DTT, 1 mM spermidine, 0.01% (v/v) Triton X-100, and 4 mM of each NTP (3). Before use, buffers were sterile-filtered using a 0.2 micron syringe filter. In experiments where several experimental conditions were tested in parallel, the same stocks of buffers, NTPs and T7 RNAP were used for all conditions. Gel filtration (GF) buffer (50 mM Tris-HCl at pH 8, 200 mM NaCl, 2 mM EDTA, 5% glycerol and 2 mM DTT) was used for storage and dilution of the in-house isolated T7 RNAP. To minimize formation of protein aggregates, we recommend diluting T7 RNAP by no more than 10-fold at a time.

It is important to place high concentration T7 RNAP reactions at 37° C. quickly after setup. We further note that while the reactions described in FIG. 1 were incubated for ˜1 day, subsequent experiments showed that turbidity and substantial RNA synthesis for no-template-added, high concentration T7 RNAP reactions set up in tubes can also be observed at much earlier time points (e.g. at ˜4 hours into incubation at 37° C.). We also note that high concentration T7 RNAP reactions exhibit a strong temperature dependence. Reactions (set up in bulk in tubes) that were maintained for a length of time at room temperature (˜25° C.) appeared as smears on denaturing gels. We have not extensively characterized the RNA products synthesized at room temperature but some sequencing results indicate that the time spent by a reaction at room temperature is correlated with the count of homopolymeric RNA sequences (specifically, poly(rA) and poly(rU)) detected in the corresponding sequenced pool.

Gel Extraction from Polyacrylamide Gels

Excised gel fragments were transferred to autoclaved, nuclease-free 0.6 ml tubes that had small cross-shaped incisions at the bottom. The 0.6 ml tubes were contained in 1.5 ml siliconized tubes. Gel fragments were shredded by centrifugation. 300-400 μl of RNA elution buffer (300 mM sodium acetate at pH 5.3, 1 mM EDTA) or DNA elution buffer (300 mM sodium chloride, 10 mM Tris-HCl at pH 8, 1 mM EDTA) (36) was added to shredded gel pieces. The specific elution buffer used depended on the nature of nucleic acid to be extracted (e.g. RNA elution buffer was used for extracting replicating RNA populations and for extracting ligated RNA during RNA-seq library preparation; DNA elution buffer was used for extracting cDNA and for extracting DNA oligos such as the reverse transcription primer used for RNA-seq library preparation). Shredded gel with elution buffer added was briefly vortexed and frozen at −80° C. for 15 minutes, followed by rocking overnight at 4° C. (for RNA) or at room temperature (for DNA). Gel was then sedimented by centrifugation, and the supernatant transferred to a new 1.5 ml siliconized tube. To ensure maximal recovery of nucleic acids, gel was further washed in 100 μl of elution buffer and centrifuged. The resultant supernatant was combined with the supernatant obtained from the previous gel centrifugation step. After a final centrifugation of the pooled supernatants to sediment any remaining gel pieces, the recovered solution was ethanol precipitated with 2.5 volumes of 100% ethanol.

RNA-Seq Protocol (See Also FIG. 7)

The basic skeletal framework for the RNA-seq protocol used in this study is based on previous work by our lab and others (e.g. “RNA-seq protocol 1” in (37) and references therein; see also (36)). We made several optimizations for efficient capture of replicating RNAs. In particular, we optimized full-length cDNA synthesis because under standard reverse transcription conditions with commonly available enzymes, no full-length cDNAs were detectable by SYBR Gold gel staining (though bands corresponding to particular truncated cDNA fragments were clearly observed). The problem of inefficient reverse transcription of the RNAs replicated by T7 RNAP was also reported previously (5). Sequencing of chemically synthesized RNA oligos (e.g. AF-NJ-223 and AF-NJ-224) served as a positive control for our protocol.

3′ ligation of ssDNA adapter to RNA: A 20 μl reaction was set up for each sample=7.6 μl RNA+2 μl 100% DMSO+6 μl 50% PEG 8000+2 μl 10×T4 RNA ligase buffer+0.4 μl 100 μM AF-NJ-269 (or AF-JA-34)+2 μl T4 RNA ligase 2, truncated, K227Q (400 units). Ligation reactions were incubated at 16° C. in a thermal cycler for 18 hours-20 hours 40 minutes. Reactions were heat-inactivated at 65° C. for 20 minutes. Ligation products were gel extracted and resuspended in 0.5×TE (pH 7.4). Note that AF-NJ-269 and AF-JA-34 have 8 and 6 degenerate bases at the 5′ end, respectively, which serve as molecular identifiers (UMIs) in downstream bioinformatic analyses.

Reverse transcription: 8 μl of the ligated RNA was heated at 95° C. for 3 minutes in a thermal cycler, followed by snap cooling on ice for 3 minutes (see Table 1 in (38)). Next, added to each reaction (on ice) was 4 μl 5× First Strand Buffer, 1 μl RNase OUT (40 units), 1 μl 0.1 M DTT and 1 μl dNTPs (10 mM each), 0.64 μl 72 ng/μl gel-extracted AF-JA-126 (concentration quantified by Qubit ssDNA kit, Thermo Fisher #Q10212) and 0.36 μl water, followed by 4 μl (800 units) of SuperScript III. Of note, the 95° C. denaturation-snap cooling step and using more SuperScript III were key optimizations for increasing yield of full-length cDNAs.

Reactions were immediately placed in a thermal cycler with a pre-heated lid and incubated at 50° C. for 2 hours 30 minutes-2 hours 40 minutes. [After cDNA synthesis, RNA can be hydrolyzed by treatment with sodium hydroxide (final concentration 0.2 N) at 70° C. for 15 minutes.] cDNA products were gel extracted and resuspended in RNase-free water.

A no-template reaction was set up in parallel each time the reverse transcription protocol was performed; no products were detected for the no-template controls.

Circularization of cDNA: 5.5 μl of the cDNA was heated at 95° C. for 3 minutes in a thermal cycler, followed by snap cooling on ice for 3 minutes. Either CircLigase reaction components or CircLigase II reaction components were then added to each reaction on ice [CircLigase reaction components: 1 μl 10× circLigase buffer+0.5 μl 50 mM MnCl₂+2 μl 5M Betaine+0.5 μl 1 mM ATP+0.5 μl circLigase enzyme (50 units); CircLigase II reaction components: 1 μl 10× circLigase II buffer+0.5 μl 50 mM MnCl₂+2 μl 5M Betaine+1 μl circLigase II enzyme (100 units)]. Reactions were immediately incubated at 60° C. for 1-2 hours, followed by heat inactivation at 80° C. for 10 minutes.

PCR: Illumina TruSeq HT indices and adapter sequences were appended using PCR. We set up 30 μl PCR reactions consisting of: 15 μl 2× Phusion Master Mix+0.3 μl 100 μM Primer 1+0.3 μl 100 μM Primer 2+1 μl circularized cDNA (reaction contents from cDNA circularization step directly used)+13.4 μl nuclease-free water. For each sample, we set up several PCR reactions with differing PCR cycle numbers, and selected for sequencing the reaction with the least number of cycles that yielded the expected product band on an ethidium bromide-stained 3.5%-4% agarose gel. The PCR cycling conditions were:

98° C., 30 seconds

For n cycles, where n is variable, perform: 98° C., 10 seconds

60° C., 10 seconds

72° C., 20 seconds-60 seconds

10° C., hold

PCR amplified RNA-seq libraries were gel-extracted using the MinElute gel extraction kit (Qiagen #28604), and quantified using the Qubit dsDNA HS kit.

All samples were sequenced on the Illumina MiSeq platform.

Note that gel electrophoresis following each of the steps of 3′ ligation, reverse transcription and PCR provided a visual assessment of reaction efficiencies for each sample we sequenced.

During sample loading on gels, samples were always separated by at least one gel lane (which was either left empty or contained a size marker) to minimize cross-contamination. For experiments where we compared template sequences with product sequences for a T7 RNAP RNA replication reaction, gel cuts for the template and product pools were made at similar sizes during RNA-seq library preparation.

Droplet Microfluidics

We used standard methods in soft lithography (39) to fabricate all microfluidic devices using a 10:1 base-to-curing agent ratio from the Sylgard 184 Silicone Elastomer kit (Dow Corning). Inlet and outlet holes were made using a 1 mm biopsy punch (Miltex), and the PDMS devices were plasma bonded to glass slides in a cleanroom.

We used a standard flow-focusing geometry with a Y-junction mixer to generate droplets (FIG. 15). The height of our droplet generation channels was 27 microns. Three syringe pumps (Kent Scientific) were used to inject the three fluid streams into our device at fixed flow rates. The aqueous droplet phase consisted of a mixture of two aqueous reagent streams which were combined at a Y-junction upstream of the flow-focusing nozzle. One aqueous reagent stream was used to flow in NTPs, PEG 8000 and any DNA/RNA template, and the other stream was used to flow in all other reagents. The continuous oil phase consisted of HFE-7500 containing 2% wt/wt 008-FluoroSurfactant. We used Aquapel (Pittsburgh, Pa.) to render the channels hydrophobic to prevent droplet wetting of the walls. Following Aquapel treatment, we carefully wrapped the droplet generation devices in aluminum foil and autoclaved on a gravity cycle. Autoclaved channels were kept wrapped in aluminum foil until use. In cases where multiple experimental conditions were tested in parallel, a separate autoclaved channel was used for each condition.

We used a flow rate of 0.1 ml/hr for each of the two aqueous drop phases (0.2 ml/hr combined flow rate) and a flow rate of 0.4 ml/hr for the continuous oil phase. We used a high-speed camera (Phantom v7.3) mounted on an inverted microscope with a 4× objective to continuously monitor droplet generation and also to record videos of the droplet formation process at 40,000 fps for measurement of droplet size. For the latter, we measured the time it took to form a single drop and calculated the droplet size based off of the combined aqueous phase flow rate of 0.2 ml/hr.

We did this for multiple drops to obtain a distribution of droplet size. Once the droplet size stabilized (after the first few minutes of drop generation), we serially collected droplets in 0.2 ml PCR tubes for assay purposes.

Bioinformatic Analysis

We have deposited all the code used in our study in a GitHub repository. A brief description of the deposited code can be found in Table 5. Other software that was additionally used for analysis included the ViennaRNA suite (40), Phylip (41), Interactive Tree of Life web interface (42), Trimmomatic (43), BWA (44) and Samtools (45). For sequence alignment of replicating RNAs, we used the classical Needleman-Wunsch (46) and Smith-Waterman algorithms (47).

FIG. 2A- and FIG. 10-Specific Protocols

To each of the RNA oligos AF-NJ-219 and AF-NJ-220, an extra adenine was added using T4 RNA ligase 1 (48) as follows: 90 μl of reaction volume containing 50 pmol of RNA oligo was denatured at 95° C. for 3 minutes followed by snap cooling on ice for 3 minutes. The reaction was removed from ice and the following reagents were quickly added: 10 μl of 100 μM pAp (in water), 15 μl of 10×T4 RNA ligase reaction buffer, 15 μl of 10 mM ATP, 15 μl of 100% DMSO and 5 μl of T4 RNA ligase 1 (50 units). Reaction incubation was at 16° C. for 22.25 hours in a thermal cycler. The reaction was stopped by addition of SDS and EDTA, followed by an extraction with 1:1 phenol-chloroform.

We used serial dilution to quantitatively compare T7 RNAP reaction yields from three template types (FIG. 2A, FIG. 10A and data not shown): (i) Y2 RNA synthetic oligos with an extra 3′ adenine, (ii) Y2 RNA synthetic oligos without an extra 3′ base and (iii) gel-extracted Y2 RNA monomer replication products. In these assays, RNA oligos with an extra 3′ adenine were far more potent than oligos without an extra base in generating replicating populations, with yields from 16-fold dilution of extra 3′ adenine containing oligos comparable to yields from undiluted oligos which did not contain an extra 3′ base. The third template type—gel-extracted Y2 RNA monomer replication products—yielded roughly similar amounts of reaction products after ˜16-32 fold dilution compared to undiluted RNA oligos with an extra 3′ adenine. Several possibilities could account for the lower template efficiency of RNA oligos with an extra 3′ adenine compared to the gel-extracted Y2 RNA monomer replication products, including (i) an uncharacterized template requirement (e.g. particular dependence on a type of RNA structure or on the 5′ chemical end of the RNA (synthetic RNA oligos have 5′ hydroxyl ends whereas replication products have 5′ triphosphate ends)), (ii) a more efficient value for a characterized template requirement (e.g. 3′ extra base combinations other than a single adenine may be more efficient for instructing RNA synthesis), and (iii) an uncharacterized growth advantage due to the complex ensemble character of the Y2 RNA replication products (see e.g. FIG. 3) versus the synthetic RNA oligos.

Quantification of gel intensities was done using the raw image data with AlphaView software (ProteinSimple). For each reaction lane, gel intensity was quantified within a bounding box made from approximately 52 to 60 nucleotides (RNA oligo input bands at ˜50 nucleotides were excluded so as not to have signal from the input template). The bounding boxes did not contain any saturated pixels. The average intensity from “blank” bounding boxes on the same gel was used for background subtraction.

For treatment of Y2 RNA replication products with RppH or SAP (FIG. 10B), RNA was first denatured at 95° C. for 3 minutes followed by snap cooling on ice for 3 minutes. Buffer components and enzymes were added subsequently. Buffer compositions for the phosphatase treatments were based on manufacturer recommendations. Phosphatase reactions were incubated at 37° C. for 1 hour followed by heat inactivation at 65° C. for 20 minutes. Prior to loading on gels, RNA was isolated by addition of SDS and EDTA, 1:1 phenol-chloroform extraction and ethanol precipitation.

FIG. 4-Specific Protocols

Replication reactions and sequencing for the X₁ (AF-NJ-257) and Y2₁ (AF-NJ-258) libraries were performed in duplicate with similar results. Starting RNA oligo template concentrations for replication of the X1 and Y21 libraries were 2 ng/μl and 4 ng/μl, respectively.

The pre-replication RNA pools for the X₂, X₃, X₄ and Y2₂ libraries were prepared by T7 RNAP-catalyzed DNA transcription of DNA oligos AF-NJ-200, AF-NJ-201, AF-JTG-11 and AF-JTG-13, respectively. In these reactions, final concentrations of AF-NJ-200 and AF-NJ-201 were 25 nM, and of AF-JTG-11 and AF-JTG-13 were ˜2.4 ng/μI.

Prior to RNA replication, the transcribed X2 and X₃ RNA pools were treated with TURBO DNase (3 μl TURBO DNase in a 50 μl reaction with 1× TURBO DNase buffer) at 37° C. for 1 hour, followed by addition of SDS and EDTA, 1:1 phenol-chloroform extraction and ethanol precipitation.

FIG. 6B-E-, FIG. 16- and FIG. 20B-Specific Protocols

Covaris shearing of DNA: DNA (in TE, pH 8) was sheared using a Covaris instrument to a size range of 100-300 bp as assessed by agarose gel electrophoresis. Sheared DNA was purified using the Zymo Clean and Concentrator kit. Column purification of DNA seeds using the Zymo Clean and Concentrator kit is expected to impose a lower limit size cutoff on the recovered DNA fragments.

Restriction digestion: 75 μl reactions with either MnII (7.5 μl) or Hpy188III (6 μl), DNA and 1× CutSmart buffer were incubated at 37° C. for 2 hours. Digests were monitored to reach near completion by agarose gel electrophoresis. Digested DNA fragments were purified using the Zymo Clean and Concentrator kit. To minimize denaturation of short dsDNA fragments, heat inactivation was not used for stopping the restriction enzyme reactions. Hpy188III and MnII were chosen as restriction enzymes because the two enzymes are expected to generate, on average, fragments of roughly similar size as fragments generated by Covaris shearing. Additionally, these two enzymes allow for generation of a diverse pool of DNA seeds because: (i) The recognition sequences and/or cleavage sites of the two enzymes contain degenerate bases, (ii) The two enzymes leave different kinds of overhangs (Hpy188III leaves 5′ overhangs and MnII leaves 3′ overhangs), and (iii) The two enzymes have different relationships between the cleavage site and recognition sequence (Hpy188III cuts at its recognition sequence whereas MnII cuts a few bases away from its recognition sequence).

Lambda DNA was Covaris sheared. The plasmid pPD122.03 was mini-prepped using the ZymoPURE Plasmid Miniprep kit, which includes an RNase A digestion step (RNase A containing buffer ZymoPURE P1 was stored at 4° C. to ensure maximal activity). The plasmid was then Covaris sheared. S. cerevisiae genomic DNA was restriction digested separately with MnII and with Hpy188III.

Genomic DNA was prepared from the nematode strains using a standard protocol involving SDS-Proteinase K treatment followed by phenol-chloroform extraction and ethanol precipitation. Genomic DNA preps (DNA amounts up to 7 μg/prep) were treated with 30 μg of RNase A (ThermoFisher) at pH 7.4 at 42° C. for 2 hours (no salt added for RNase A treatment), followed by Proteinase K-SDS treatment and 2 extractions with 1:1 phenol-chloroform. No gel density corresponding to RNA was visible by agarose gel electrophoresis following RNase A digestion. C. elegans DNA was then Covaris sheared, C. remanei DNA digested with MnII and C. brenneri DNA digested with Hpy188III.

The predefined DNA seed pool consisted of seven types of DNA seeds (percentage contribution by mass given): (i) Sheared lambda phage genomic DNA (7%), (ii) Sheared C. elegans genomic DNA (7%), (iii) Sheared DNA from the plasmid pPD122.03 (7%), (iv) MnII digested C. remanei genomic DNA (20%), (v) Hpy188III digested C. brenneri genomic DNA (15%), (vi) MnII digested S. cerevisiae genomic DNA (19%), and (vii) Hpy188III digested S. cerevisiae genomic DNA (25%). After pooling the seven types of DNA seeds together, the combined DNA seed pool was treated with 100 units of RNase 1 in the presence of 100 mM NaCl at pH 8 at 37° C. for 1 hour. RNase I was removed using 0.2% SDS treatment followed by 2 extractions with 1:1 phenol-chloroform6. A “No RNase I control” was used to confirm that RNase 1 treatment did not lead to loss of DNA.

The DNA seed pool was then split into three equal parts: (i) No further treatment (except for addition of TURBO DNase buffer to 1× final concentration), (ii) Treatment with 3 μI TURBO DNase (in a 50 μl reaction with 1× TURBO DNase buffer) at 37° C. for 1 hour, and (iii) Heating with sodium hydroxide (0.2 N; reaction volume was 10 μl) at 70° C. for 1 hour. For neutralization of the sodium hydroxide, 20 μl 200 mM Tris-HCl at pH 7 was added.

After the respective treatments to the three parts of the DNA seed pool, SDS and EDTA were added to each part, followed by extraction with 1:1 phenol-chloroform and ethanol precipitation.

The efficacy of TURBO DNase treatment of the DNA seed pool was assessed by measuring DNA concentrations for the 1st (no DNase treatment) and 2nd parts (+DNase treatment) of the seed pool. DNase treatment was found to reduce DNA amount by ˜50 fold.

T7 RNAP reactions were set up in drop and tube format for four experimental conditions in parallel: (1) Unseeded, (2) Seeded with DNA pool, (3) Seeded with DNase-treated DNA pool and (4) Seeded with hot alkali-treated DNA pool. For the “Seeded with DNA pool” condition, the volume seeded with the 1st part of the DNA seed pool (neither DNase nor NaOH treated) gave a final DNA seed reaction concentration of ˜47 femtograms per μl (estimated to correspond to ˜10-15 molecules of DNA seeds per droplet); an equivalent volume of the 2nd and 3rd parts of the DNA seed pool was seeded for the “Seeded with DNase-treated DNA pool” and “Seeded with hot alkali-treated DNA pool” conditions, respectively. Each replicate of drop reactions for an experimental condition consisted of ˜50 μl total volume (drops+oil) and took ˜5 minutes for generation.

The MS2-spike in was created by fragmentation of bacteriophage MS2 genomic RNA in a solution of 5 mM Na₂CO₃, 45 mM NaHCO₃ and 1 mM EDTA at 95° C. for 30 minutes (49). MS2 fragments in the 70-90 nucleotides size range were gel-extracted and subsequently 3′ dephosphorylated by T4 PNK treatment in 100 mM MES-NaOH (pH 5.4), 10 mM MgCl₂, 10 mM beta-mercaptoethanol and 300 mM NaCl, at 37° C. for 6 hours (49); this was followed by purification using the NEB Monarch RNA Cleanup kit (NEB #T2030S), and then by an extraction with 1:1 phenol-chloroform and ethanol precipitation. 60 picograms of the prepared MS2-spike in was added to the aggregated drop reaction products for sequencing, and 300 picograms to the tube reaction products.

FIG. 17-Specific Protocols

Four experimental conditions were set up in parallel: (1)+Template, −T7 RNAP; (2) −Template, +T7 RNAP; (3)+Template, +T7 RNAP; (4)+Template (diluted 10 fold), +T7 RNAP. SYBR Gold was included in reactions for all four conditions at a final concentration of 1×. AF-NJ-223 was used as template for conditions (1), (3) and (4) at a final concentration of 0.1 pM, 0.1 pM and 0.01 pM, respectively. Reactions were kept covered with aluminum foil during incubation.

Bright-field and fluorescence images of drops were acquired in 30 micron tall microfluidic wells using an epifluorescence microscope (Nikon Ti-U) equipped with an electron multiplying CCD camera (Andor). We used an excitation filter with transmission centered at 470 nm and an emission filter with transmission centered at 525 nm. An exposure time of 0.2 s was used during imaging.

Percentage drops fluorescent for a field of view was calculated by using the fluorescence and bright-field images for the field of view. Specifically, percentage drops fluorescent was calculated as the ratio of the number of drops detected in the fluorescence image to the number of drops detected in the bright-field image. Images for all four experimental conditions were processed using the same parameters. Automated detection of drops was checked by visual inspection.

Best Practices for Conducting T7 RNAP-Catalyzed RNA Replication Reactions

Best laboratory practices for minimizing cross-contamination when working with nucleic acid amplification technologies (e.g. (50)) also apply to the study and use of T7 RNAP-catalyzed RNA replication. Amplification of contaminating templates could be harder to control with T7 RNAP-catalyzed RNA replication compared to PCR because (i) no primers are required for RNA replication, and (ii) amplification proceeds continuously during RNA replication as opposed to in discrete cycles during PCR. Amplification of contaminating RNA replicons that are not part of an input template pool but are pre-existing in the laboratory can be minimized using droplet microfluidics as contaminants could be confined to a few drops. We further highlight key best practices for studying T7 RNAP-catalyzed RNA replication using bulk tube reactions below:

To prevent contamination of T7 RNAP preps with RNA replicons, we highly recommend that the polymerase preps be isolated in a facility which does not receive any shipments from the facility where experiments on RNA replication have been or are being conducted. Contamination of polymerase preps with a pre-existing replicon will lead to subsequent no-template-added, high concentration T7 RNAP reactions consistently yielding that particular replicon because templated replication occurs more efficiently than evolution of a novel replicon (see e.g. (5)).

Maintain a catalogue of which RNA replicon sequences have already been isolated in the laboratory and when these were isolated. If a no-template-added, high concentration T7 RNAP reaction yields a sequence similar to what has previously existed in a laboratory, then it cannot be ascertained whether the new reaction witnessed molecular evolution or amplified a pre-existing template.

When studying templated RNA replication, conduct reactions at low concentration of T7 RNAP and for short durations of time (˜few hours). Also perform no-template-added controls in parallel and check that no products are detected for these controls.

TABLE 1 Reference sequences for the RNA species described in FIG. 1. RNA Reference Sequence Number Sequence 1.1 (SEQ ID NO: 1) CCAUAAUUAUUGUAUGACACU GGCCAAUAAUUAUUGUAUAU UGGCCAGUGUCAUACAAUAA UUUUCC 2.1 (SEQ ID NO: 2) GGAAAAUAUACAUAUUGAAGG UGUGUAUGUAUAUUUGUAU AUUCACAAAAAUAUACAUACA CACCUUCAAUAUGUAUAUUA UUGG 2.2 (SEQ ID NO: 3) CCAUAAUGUGAAUGCGCGUCG CCUUGGCGCUGAUUUGCG UUAAUUGGGAAUUAACGCAAA UC 3.1 (SEQ ID NO: 4) CCCCAAAAUUAUUGUAUGGCA CUGGCCCCAUUCAAUAAUU GAAAAUUAUUGAAUGGGGCCA GU 3.2 (SEQ ID NO: 5) CCAAAAUUAUUGUAUGGCACU GGCCCCAUUCAAUAAUUAU UGUAUGGCACUGGCCCCAUUC AAUAAUUUUCAA 4.1 (SEQ ID NO: 6) GGGAAAAAUUAUUGUAUGGCA CAACAAUAAUUUUCGUAAAA UUAUUGUUGUGCCAUACAAUA AUUUAUGG 4.2 (SEQ ID NO: 7) GGGGAAAAAAUUAUCACUCGC CGGAUAAUUUCUCCUAGAA AUUAUCCGGCGAGUGAUAAUU UCUGG 4.3 (SEQ ID NO: 8) CCAUAAUUAUUGUAUGGCUCG UACAAUAAUUAUUAUUAUUA UUAAUAAUUAUUUAAUAAUAA AUUAUUGUACGAGCCAUACA AUAAUUUUCC 5.1 (SEQ ID NO: 9) GGUAAAUUAAUGUUCUUAACA CUACCAUUAAUUUACAAAAU UAAUGGUAGUGUUAAGAACAU UAAUUUUGG 6.1 (SEQ ID NO: 10) GGGAAAAAUUUAUUAUUUUCU UGGAAAUUUAUUAUUUUCU UGGAAAUUUAUUAAAUAAUAA AUUUCCAAGGAAAUAAUAAA UUUCCAAGAAAAUAAUAAAUU UUGGG 7.1 (SEQ ID NO: 11) CCGAAAAUUAUUGUAUGGCAC ACAACAAUAAUUUUUCGUGA AAAUUAUUGUUGUGUGCCAUA CAAUAAUUUUAUUC 7.2 (SEQ ID NO: 12) CCGAAAUUAUUGUAUGUCGUC ACAAUAAUUUUCGACGAAAA UUAUUGUGACGACAUACAAUA AUUUUUCC 8.1 (SEQ ID NO: 13) GGGAAAAAUAAUACAUUUGGU GUCGGAUAAUGUAUUAUUU CAAAUAAUACAUUAUCCGACA CCAAAUGUAUUAUUUAUGG 9.1 (SEQ ID NO: 14) GGGAAAAAUUAUUGUAUGGCU CGUCAAUAAUUUUUGUCCA AAAUUAUUGACGAGCCAUACA AUAAUUUUGGG 10.1 (SEQ ID NO: 15) GGAAUAAUUAUUUGUUGUACU AGGAAUAAUUAUUUACAAAA UAAUUAUUCCUAGUACAACAA AUAAUUAUUAGG 11.1 (SEQ ID NO: 16) GGGAAAAAUUAUUGUAUGGCA CACAAUAAUUUUCAUUAUU GUGUGCCAUACAAUAAUUUUG GG 12.1 (SEQ ID NO: 17) CCCCAAAAUUUCAAGAUCAGG GCUUGAAAUUUUGUAAAAUU UCAAGCCCUGAUCUUGAAAUU UUCC 13.1 (SEQ ID NO: 18) GGGAAAAAUUAUUGUAUGUCU CAACAAUAAUUUUCGUGAAA AUUAUUGUUGAGACAUACAAU AAUUUUGGG 14.1 (SEQ ID NO: 19) GGGAAAAAUUUCAAGAUCAGG GAUUGAAAUUUUACAAAAUU UCAAUCCCUGAUCUUGAAAUU UUGGG 14.2 (SEQ ID NO: 20) GGGAAAAAUUAUUGUAUGGCC ACAAUAAUUUUCGAAAAAUU AUUGUGGCCAUACAAUAAUUU UGGG 15.1 (SEQ ID NO: 21) GGGAAAAAAUUAUUGUAUGGC AAAUAAUUUUUCACGAAAAU UAUUUGCCAUACAAUAAUUUU CGG 15.2 (SEQ ID NO: 22) GGGAAAAAAUUAUUGUAUGGC UCACAAUAAUUUUCUCGAAA AUUAUUGUGAGCCAUACAAUA AUUUUCGG 16.1 (SEQ ID NO: 23) CCAAUUAUACUCUACCCAACU GAGGGUAUAAUAUGGUAAU UAUACCCUCAGUUGGGUAGAG UAUAAAUUCC 17.1 (SEQ ID NO: 24) GGGAAAAAUUAUUGUAUGGCA AACCAAUAAUUUUCGUCAAA AUUAUUGGUUUGCCAUACAAU AAUUUUGGG 18.1 (SEQ ID NO: 25) CCAUAAUUAUUGUAUGGCUCG UACAAUAAUGAAAAUUAUUG UACGAGCCAUACAAUAAUUUU CC 18.2 (SEQ ID NO: 26) CCAUAAAUAUUUCUCCUAGGG CAAUGAAAUAUUAUGGAUCA UAAUAUUUCAUUGCCCUAGGA GAAAUAUUAUCC 19.1 (SEQ ID NO: 27) GGGAAAAAUUACACUUUUCGC AUCUUUGUGUAAUUUUUGU GAAUAAAUUACACAAAGAUGC GAAAAGUGUAAUUUAUGG 20.1 (SEQ ID NO: 28) CCAAUAAUACAAAUAUUUCCU CAUCCUCAUUUGUAUUAUAA UACAAAUGAGGAUGAGGAAAU AUUUGUAUUAUAAUCC 21.1 (SEQ ID NO: 29) GGGAAAAAUUAUUGUAUGGCA CAAACAAUAAUAAUUUUCUU UAAAAAUUAUUGUUUGUGCCA UACAAUAAUUUUGGG 22.1 (SEQ ID NO: 30) GGGAAAAAUUAUUGUAUGGCA CACAAUAAUUUUUAACAAAA UUAUUGUGUGCCAUACAAUAA UUUUGGG 23.1 (SEQ ID NO: 31) GGGAAAAAUUAUUGUAUGGCA CAACAACAAUAAUUUUCGUA AAAUUAUUGUUGUUGUGCCAU ACAAUAAUUUAUGG 24.1 (SEQ ID NO: 32) GGGAAAAAUUUCAAGAUCAGG GGCUUGAAAUUUUACAAAA UUUCAAGCCCCUGAUCUUGAA AUUUUGGG NB: (i) Short 5′ and 3′ base extensions (of one or a few bases) may be present in the sequences for reasons discussed in the text. (ii) A few sequences may not be full-length because particular truncated cDNAs or prematurely terminated 17 products were predominant in the sequenced pool. E.g. Sequence 3.1 reported for reaction 3 is unlikely to be a full-length sequence. The RNA species for reaction 3 were not efficiently reverse transcribed, which makes detection of the full-length sequences more challenging.

TABLE 2 Sequences of RNA species described in FIGS. 6B-6E and FIG. 20B. RNA species Sample information number Sequence Unseeded, Aggregated 1 GGAUAAUUAUUAUCAUUGAUCAUCAAUGAUGAUG Drop Reaction, 1 day time AAUUAUUAUCAUUGAUGAUCAAUGAUAAUAAUUAU point GG (SEQ ID NO: 33) Unseeded, Aggregated 2 GGAAAAAUAAUUAUUCUUGCUGUAGAAAUAAUUAU Drop Reaction, 1 day time UCCGAAUAAUUAUUUCUACAGCAAGAAUAAUUAUU point UCGG (SEQ ID NO: 34) Unseeded, Aggregated 3 GGAAGAAACAUUGUCAAUUGCCUUGGCCCAAUGU Drop Reaction, 1 day time UUCCUGAAACAUUGGCCAAGGCAAUUGACAAUGU point UUCAUGG (SEQ ID NO: 35) Unseeded, Aggregated 4 GGAUAAACUUUCUUUCAUUCUGUCUAAGAAAGUU Drop Reaction, 1 day time UAAACAGAGUUUUAAACUUUCUUAGACAGAAUGAA point AGAAAGUUUAAGG (SEQ ID NO: 36) Unseeded, Aggregated 5 GGAAUAAUAAUAAUUCUAAGUAAGAGUUAUAUUAA Drop Reaction, 1 day time UACAUAAUUUCAAAUUAUGUAUUAAUAUAACUCUU point ACUUAGAAUUAUUAUUCGG (SEQ ID NO: 37) Unseeded, Aggregated 6 GGAAUUUUAAAUUAUUUAAAUGGAAUUUCCAUUUA Drop Reaction, 1 day time AUAUUAAUUAAAUGGAAAUUCCAUUUAAAUAAUUU point AAAAAUGG (SEQ ID NO: 38) Unseeded, Aggregated 7 GGAUAAUAUUUCAAUAUUCCAUUUUAUUAUUGAAA Drop Reaction, 1 day time UUGUAAUAUUUCAAUAAUAAAAUGGAAUAUUGAAA point UAUUUUGG (SEQ ID NO: 39) Unseeded, Aggregated 8 GGAUUAAUUAAUUGAUUCAUAAUUAAUUAAUUGAA Drop Reaction, 1 day time UAAUUAAUUAUGAAUCAAUUAAUUAUGG point (SEQ ID NO: 40) Unseeded, Aggregated 9 GGAAAAAUUAAAUAUAGUUCCAGUUUCUCCUAUAU Drop Reaction, 1 day time UUAAUUAGAAAUUAAAUAUAGGAGAAACUGGAACU point AUAUUUAAUUUCUGG (SEQ ID NO: 41) Unseeded, Aggregated 10 GGAAAAUUUCAAGAUCAGGGCUUGAAAUUUUACA Drop Reaction, 1 day time AAAUUUUCAAGCCCUGAUCUUGAAAUUUUGGGG point (SEQ ID NO: 42) Unseeded, Aggregated 11 GGUUAAAUAUUAUUGAAAUCUCAAAAUAAUAAAAC Drop Reaction, 1 day time CAAAUAUUAUUUUGAGAUUUCAAUAAUAUUUGG point (SEQ ID NO: 43) Seeded with DNA pool, 1 GGAAUUAUCAUUUCUUGCAGAUAAAGAUGAUAAU Aggregated Drop Reaction, CCAAUUAUCAUCUUUAUCUGCAAGAAAUGAUAAUU 1 day time point GG (SEQ ID NO: 44) Seeded with DNA pool, 2 GGAAAAUAUUAUUUUCAAGCUAUAUCUAAUAAUAU Aggregated Drop Reaction, UUUGCCAAAAUAUUAUUAGAUAUAGCUUGAAAAUA 1 day time point AUAUUUUGG (SEQ ID NO: 45) Seeded with DNA pool, 3 GGAAUAUUUCAUUGAUGAAAUUACAAUGAUCAAUG Aggregated Drop Reaction, AAUAUUUCAUUGAUCAUUGUAAUUUCAUCAAUGAA 1 day time point AUAUUGG (SEQ ID NO: 46) Seeded with DNA pool, 4 GGAAAAAAUUCUUUUCAGAAAUGAAUUGAAAUUCU Aggregated Drop Reaction, UUUCAAUUCAUUUCUGAAAAGAAUUUUUGG 1 day time point (SEQ ID NO: 47) Seeded with DNA pool, 5 GGAAAAAUUGUAUCUAUCCAAUUUUGAUACAAAAU Aggregated Drop Reaction, UGUAUCAAAAUUGGAUAGAUACAAUUUUGG 1 day time point (SEQ ID NO: 48) Seeded with DNA pool, 6 GGAAAAUAUCAAUAAUUUCCGAUUAUUAUUGAUAA Aggregated Drop Reaction, AAUAUCAAUAAUAAUCGGAAAUUAUUGAUAUUUUA 1 day time point UGG (SEQ ID NO: 49) Seeded with DNA pool, 7 GGAAAAAUUGAAAAGUCCAAUUCAAUUUAACCAAA Aggregated Drop Reaction, AUUGAAUUGGACUUUUCAAUUUUGG 1 day time point (SEQ ID NO: 50) Seeded with DNA pool, 8 GGAAAUUUGGAUUUGGUAAAUUCUCCAAAAUUUC Aggregated Drop Reaction, CGAAAUUUUGGAGAAUUUACCAAAUCCAAAAUUGG 1 day time point (SEQ ID NO: 51) Seeded with DNA pool, 9 GGAAAAUCUUGUCAUGAAUCAAUAGAUUUUCUUG Aggregated Drop Reaction, UCAUGAAAUCUAUUGAUUCAUGACAAGAUUUUGG 1 day time point (SEQ ID NO: 52) Seeded with DNA pool, 10 GGAUAUAUAUAUAUGUGUGUGUGUGUAUAUAUAU Aggregated Drop Reaction, UCCGAUGAAUAUAUAUACACACACACACAUAUAUA 1 day time point UAUCGG (SEQ ID NO: 53) Seeded with DNA pool, 11 GGAUAAAUUAAAUAGGUUUCUGACUUUGUUAUUC Aggregated Drop Reaction, CUAUUUAAUCGGGAUUAAAUAGGAAUAACAAAGUC 1 day time point AGAAACCUAUUUAAUUUUGG (SEQ ID NO: 54) Seeded with DNA pool, 12 GGAAAAUAUGUCAUACAUUGGUCAGAGAAAAUGU Aggregated Drop Reaction, AUGUCAUACAUUUUCUCUGACCAAUGUAUGACAU 1 day time point AUUUAGG (SEQ ID NO: 55) Seeded with DNA pool, 13 GGAAAAAUUCAAAUCAAUUGCCGAUGAUUUGAUU Aggregated Drop Reaction, UUUCAUUCAAAUCAUCGGCAAUUGAUUUGAAUUU 1 day time point GGGG (SEQ ID NO: 56) Seeded with DNA pool, 14 GGAUUAAAUUUCAUAUUGUUAAUAUUUAUUAAUGU Aggregated Drop Reaction, AUGUACAAUAUGAAAUUUCAUAUUGUACAUACAUU 1 day time point AAUAAAUAUUAACAAUAUGAAAUUUCGG (SEQ ID NO: 57) Seeded with DNA pool, 15 GGAAAAAUUUAAUAGGAGUUCAGUUUAUUCUAUU Aggregated Drop Reaction, AAAUUUCCGGAAAUUUAAUAGAAUAAACUGAACUC 1 day time point CUAUUAAAUUUUGG (SEQ ID NO: 58) Seeded with DNA pool, 16 GGAAAUUUAUUUGAGAGUUGUUCCAAAUAAAUUU Aggregated Drop Reaction, UCGGAAAAUUUAUUUGGAACAACUCUCAAAUAAAU 1 day time point UUUGG (SEQ ID NO: 59) Seeded with DNA pool, 17 GGAAAAAAUUUCUUCUUCGAGAAAUUUGAAUUCCA Aggregated Drop Reaction, AAUUUCUCGAAGAAGAAAUUUUGGG 1 day time point (SEQ ID NO: 60) Seeded with DNA pool, 18 GGAAAGAAUGUUUUCAUAAGGUACAACAUUCUUU Aggregated Drop Reaction, UUCUAAAGAAUGUUGUACCUUAUGAAAACAUUCUU 1 day time point CAGG (SEQ ID NO: 61) Seeded with DNA pool, 19 GGAAAAUUUAAAUGUGCACUCCAUAUUCUCCGCA Aggregated Drop Reaction, UUUAAAUUUUCCAUAUUCAAAUGCGGAGAAUAUG 1 day time point GAGUGCACAUUUAAAUUUGGG (SEQ ID NO: 62) Seeded with DNA pool, 20 GGAAAUUGAAUAAGACUUUCCCUUAUUCAUUAAAA Aggregated Drop Reaction, UUGAAUAAGGGAAAGUCUUAUUCAAUUUGG 1 day time point (SEQ ID NO: 63) Seeded with DNA pool, 21 GGAAGAAAUCAGAAUAUUCUCCUUUUUCUGAUUU Aggregated Drop Reaction, UCUGAAGAAAAUCAGAAAAAGGAGAAUAUUCUGAU 1 day time point UUCUUGGG (SEQ ID NO: 64) Seeded with DNA pool, 22 GGAAAAUGAUUUCCUCAUUAGUUGAUCAUCAAAAU Aggregated Drop Reaction, GAUUUCAACUAAUGAGGAAAUCAUUUUGGG 1 day time point (SEQ ID NO: 65) Seeded with DNA pool, 23 GGAAAUUUAAAUGUGCCAUGAAUAUGGAAAUUUAA Aggregated Drop Reaction, AUGUGCUUUUAAAUUUCCAUAUUCAUGGCACAUU 1 day time point UAAAUUUGG (SEQ ID NO: 66) Seeded with DNA pool, 24 GGAAAAAAAUUCUGAUCGUAGUAGGAUUUCAGAA Aggregated Drop Reaction, UUUUCUUCCGAAAAUUCUGAAAUCCUACUACGAU 1 day time point CAGAAUUUCGG (SEQ ID NO: 67) Seeded with DNA pool, 25 GGAAAUAUACAAUUCUAUAUCAUUCCAUGAUAUAG Aggregated Drop Reaction, AAUAUAGAAUUGUAAAUAUACAAUUCUAUAUUCUA 1 day time point UAUCAUGGAAUGAUAUAGAAUUGUAUAUUUGGG (SEQ ID NO: 68) Seeded with DNA pool, 26 GGAAAAUUCAAAAUUGAAUUGAAUUUGGAUUUUU Aggregated Drop Reaction, CCAAAUUCAAUUCAAUUUUGAAUUUGGG 1 day time point (SEQ ID NO: 69) Seeded with DNA pool, 27 GGAUGAUUAUUUCAUGUGUCUCUAAUGAUCUAAA Aggregated Drop Reaction, CAUUAGAUCAUUAGAGACACAUGAAAUACUGG 1 day time point (SEQ ID NO: 70) Seeded with DNA pool, 28 GGGAAUAUUAAUUCAAAUUCAAUAUUGGUGUAAUA Aggregated Drop Reaction, UUAAUUCAAAUUACACCAAUAUUGAAUUUGAAUUA 1 day time point AUAUUGG (SEQ ID NO: 71) Seeded with DNA pool, 29 GGAUGAUUUGAUACAUAUUCGUUUCUAUGUAUUU Aggregated Drop Reaction, AACAAAUCAUCUUUGAUGAUUUGUUAAAUACAUAG 1 day time point AAACGAAUAUGUAUCAAAUCUUGG (SEQ ID NO: 72) Seeded with DNA pool, 30 GGAAAAAUCAAGUGUCACUUUCUCCCACUUGAUU Aggregated Drop Reaction, UUGUCAAUCAAGUGGGAGAAAGUGACACUUGAUU 1 day time point UUGG (SEQ ID NO: 73) Seeded with DNA pool, 31 GGAAAAAAUUCAAGAAUCCUCUUCUUGAAUCUUGA Aggregated Drop Reaction, AUUUUCAAAAUUCAAGAUUCAAGAAGAGGAUUCUU 1 day time point GAAUUUUGG (SEQ ID NO: 74) Seeded with DNA pool, 32 GGAAAAUAUCAACUCGAUAUUUGAUAUUUAUUCCA Aggregated Drop Reaction, AAUAUCAAAUAUCGAGUUGAUAUUUUGGG 1 day time point (SEQ ID NO: 75) Seeded with DNA pool, 33 GGAAAAUUCAAACGAUCACCUUCGUUUUGAUUUG Aggregated Drop Reaction, UCAAUUCAAACGAAGGUGAUCGUUUGAAUUUAGG 1 day time point (SEQ ID NO: 76) Seeded with DNA pool, 34 GGAUGAAUAUAUUUGUUUUGACUCCAUUCUACAA Aggregated Drop Reaction, AUAUAUUCCGAAUAUAUUUGUAGAAUGGAGUCAAA 1 day time point ACAAAUAUAUUCUGG (SEQ ID NO: 77) Seeded with DNA pool, 35 GGAAAUUAAGAUUUUUUCUCCUUUCUAAAUCUUAA Aggregated Drop Reaction, UUUUACAAAUUAAGAUUUAGAAAGGAGAAAAAAUC 1 day time point UUAAUUUGG (SEQ ID NO: 78) Seeded with DNA pool, 36 GGGAAAAUUAACAAUAUUCUUUCGAUUGUUCAAUA Aggregated Drop Reaction, UUGAAAUUUUCCAAUUAACAAUAUUGAACAAUCGA 1 day time point AAGAAUAUUGUUAAUUUGG (SEQ ID NO: 79) Seeded with DNA pool, 37 GGAAAAAACAAUUCAAUCAAUUCGUCAUGAUUGAA Aggregated Drop Reaction, ACAAUUCAAUCAUGACGAAUUGAUUGAAUUGUUU 1 day time point UUGG (SEQ ID NO: 80) Seeded with DNA pool, 38 GGAAAAAUUAAUUUGAAUAAUUAAUUUCUUCUUAA Aggregated Drop Reaction, UUUCUUCCAAUUAAUUAAGAAGAAAUUAAUUAUUC 1 day time point AAAUUAAUUUUUGGG (SEQ ID NO: 81) Seeded with DNA pool, 39 GGAAAAAAUUCAUUCGGAUUUUGUGCGAAUGAAA Aggregated Drop Reaction, UUCAUUCGCACAAAAUCCGAAUGAAUUUGGGGG 1 day time point (SEQ ID NO: 82) Seeded with DNA pool, 40 GGUUAUAUAUAUAUUGAUCCUUGCAAUAUAUAAUU Aggregated Drop Reaction, AUAUAUUGCAAGGAUCAAUAUAUAUAUUGG 1 day time point (SEQ ID NO: 83) Seeded with DNA pool, 41 GGAAUUCAAUGAGAAAAAAUCUCCCACUCAUUGAU Aggregated Drop Reaction, UCCCAAUUCAAUGAGUGGGAGAUUUUUCUCAUUG 1 day time point AAUUGGG (SEQ ID NO: 84) Seeded with DNA pool, 42 GGAAAAAUUUCAGAAUUUCUUCAUCCUCUGAAAUU Aggregated Drop Reaction, UUCUCAAAAUUUCAGAGGAUGAAGAAAUUCUGAAA 1 day time point UUUCGGG (SEQ ID NO: 85) Seeded with DNA pool, 43 GGAUAAAUACCAUAACGUUGAAUAUGAAGGUAUUA Aggregated Drop Reaction, UCCAAAAUACCUUCAUAUUCAACGUUAUGGUAUUU 1 day time point UGG (SEQ ID NO: 86) Seeded with DNA pool, 44 GGAAAAAAUUGGAUGAGAAAGUUAAAAUUAUUCAA Aggregated Drop Reaction, UUUUCCGAAAAUUGAAUAAUUUUAACUUUCUCAUC 1 day time point CAAUUUUCGG (SEQ ID NO: 87) Seeded with DNA pool, 45 GGAAUAUUAACAAAGAUAGGGAUAAGAAUGUAAUC Aggregated Drop Reaction, UUUUGUUGAAUAUUAACAAAGAUUACAUUCUUAUC 1 day time point CCUAUCUUUGUUAAUAUUGG (SEQ ID NO: 88) Seeded with DNA pool, 46 GGAAAAUUCAAAUUCAAGAUUGGAUUCUCUUGAA Aggregated Drop Reaction, UUUCAAAAUUCAAGAGAAUCCAAUCUUGAAUUUGA 1 day time point AUUUGGG (SEQ ID NO: 89) Seeded with DNA pool, 47 GGAUUGUUAUCAAUGUAUUCUUCCAAACAUUGAA Aggregated Drop Reaction, CAAUGUAUCAAUGUUUGGAAGAAUACAUUGAUAAC 1 day time point AUGGG (SEQ ID NO: 90) Seeded with DNA pool, 48 GGAAAAUAAUUUCCAAAUCAAAAUUAUUUGAUUUC Aggregated Drop Reaction, CAAAUCAAAUAAUUUUGAUUUGGAAAUUAUUUGG 1 day time point (SEQ ID NO: 91) Seeded with DNA pool, 49 GGAAAAAAUCAUUUCUCUAAUGCAAUUCAGAGAAU Aggregated Drop Reaction, GAAUAAAUCAUUUUCUCUGAAUUGCAUUAGAGAAA 1 day time point UGAUUUAUUGG (SEQ ID NO: 92) Seeded with DNase-treated 1 GGAAGAAUUUAAUUUCAUCCUCUUAAAUUCUUUAA DNA pool, Aggregated Drop ACCAAGAAAUUUAAGAGGAUGAAAUUAAAUUCUUG Reaction, 1 day time point G (SEQ ID NO: 93) Seeded with DNase-treated 2 GGAAAAUUAAAGUUCAAUGCAAUUUAAUUUUCCAA DNA pool, Aggregated Drop AAUUAAAUUGCAUUGAACUUUAAUUUUGG Reaction, 1 day time point (SEQ ID NO: 94) Seeded with DNase-treated 3 GGAAUUAAUUUAGUCUAGGUGGAACUAAUUAUAC DNA pool, Aggregated Drop UAAUUAAUUUAGUUCCACCUAGACUAAAUUAAUUA Reaction, 1 day time point GG (SEQ ID NO: 95) Seeded with DNase-treated 4 GGAGAAUUUAAAUCAUUAUCUUCUUUGAUUUAAAU DNA pool, Aggregated Drop UUAUGGCCAUAAAUUUAAAUCAAAGAAGAUAAUGA Reaction, 1 day time point UUUAAAUUCUGG (SEQ ID NO: 96) Seeded with DNase-treated 5 GGAAAUUUCAAUUCAAUGGGUUGUAUUAAUUGAA DNA pool, Aggregated Drop AUUGCCCAAUUUCAAUUAAUACAACCCAUUGAAUU Reaction, 1 day time point GAAAUUGG (SEQ ID NO: 97) Seeded with DNase-treated 6 GGAAAAUAUCAACUCGAUAUUUUGAUAUUUAUUCC DNA pool, Aggregated Drop AAAUAUCAAAUAUCGAGUUGAUAUUUUGG Reaction, 1 day time point (SEQ ID NO: 98) Seeded with DNase-treated 7 GGAAUUGAAUGGAAUGGACAAAUUCCAUAUGAUU DNA pool, Aggregated Drop CCAAUUCAUAUGGAAUUUGUCCAUUCCAUUCAAU Reaction, 1 day time point UGG (SEQ ID NO: 99) Seeded with DNase-treated 8 GGAUAAUCAUUAUCAAAUGGGAAUCUGAUAAUGA DNA pool, Aggregated Drop UGAUUAAUCAUUAUCAGAUUCCCAUUUGAUAAUGA Reaction, 1 day time point UUCUGG (SEQ ID NO: 100) Seeded with DNase-treated 9 GGAAUCAAAUAGAAUCCAUUAUCUAUUUGAUUCAA DNA pool, Aggregated Drop UCAAAAUAGAUAAUGGAUUCUAUUUCGG Reaction, 1 day time point (SEQ ID NO: 101) Seeded with DNase-treated 10 GGAAAAUUUCUAAAUAUUACUGAUCAUCAGUAAUC DNA pool, Aggregated Drop UAAAUAUUACUGAUGAUCAGUAAUAUUUAGAAAUU Reaction, 1 day time point UGG (SEQ ID NO: 102) Seeded with DNase-treated 11 GGAAUGUAAUAAAUUAUUGUUAUAUUCACUCCAAU DNA pool, Aggregated Drop GUAAUAAAUUACAUUGGAGUGAAUAUAACAAUAAU Reaction, 1 day time point UUAUUACAUUGG (SEQ ID NO: 103) Seeded with DNase-treated 12 GGAUUAUUUUAUUCAAUCUUCAUAACACCGGAAG DNA pool, Aggregated Drop AUUUAUUCAAUCUUCCGGUGUUAUGAAGAUUGAA Reaction, 1 day time point UAAAAUAAUGG (SEQ ID NO: 104) Seeded with DNase-treated 13 GGAAUUUCAAUUUCUCAUCUUGUAUAUAAAUACAA DNA pool, Aggregated Drop UUUCUCAUCUUGAAAAUGUAUUUAUAUACAAGAUG Reaction, 1 day time point AGAAAUUGAAAUUGG (SEQ ID NO: 105) Seeded with DNase-treated 14 GGAAAAUUCAAAUUGCAGUAGAUAUUGAAUUUUU DNA pool, Aggregated Drop UUCCAAAAUUCAAUAUCUACUGCAAUUUGAAUUUU Reaction, 1 day time point GGG (SEQ ID NO: 106) Seeded with DNase-treated 15 GGAUAAAUUGAUAGGAACAAUUAAUAGUGUCAAUU DNA pool, Aggregated Drop UAUCCGAUAAAUUGACACUAUUAAUUGUUCCUAUC Reaction, 1 day time point AAUUUAGGG (SEQ ID NO: 107) Seeded with DNase-treated 16 GGGAAAAAUCAAGUUCUGAGUUUUGAUUUAUCCA DNA pool, Aggregated Drop AAAAUCAAAAAACUCAGAACUUGAUUUUUGG Reaction, 1 day time point (SEQ ID NO: 108) Seeded with DNase-treated 17 GGAAGAUUGAAAAUCUUAUAAUAUCUAAGAGAUAG DNA pool, Aggregated Drop AUUUUCAUGAUUGAAAAAUCUAUCUCUUAGAUAUU Reaction, 1 day time point AUAAGAUUUUCAAUCAUGG (SEQ ID NO: 109) Seeded with DNase-treated 18 GGAAAAAUUAUUACAAUGCACCCAUAUCAUUGUAA DNA pool, Aggregated Drop UUUGAAAUUAUUACAAUGAUAUGGGUGCAUUGUA Reaction, 1 day time point AUAAUUUCGG (SEQ ID NO: 110) Seeded with DNase-treated 19 GGAAGAUGAAUAUGUUAAUUAGCUUAAUCAU UCC DNA pool, Aggregated Drop AUAUUCAUCCGAUGAAUAUGGAAUGAUUAAGCUAA Reaction, 1 day time point UUAACAUAUUCAUCAUGG (SEQ ID NO: 111) Seeded with DNase-treated 20 GGAAAAUUAUCUGUUCAAAUUCAAAUGAUGAUUUU DNA pool, Aggregated Drop CCAAAUUAUCAUUUGAAUUUGAACAGAUAAUUUGG Reaction, 1 day time point (SEQ ID NO: 112) Seeded with DNase-treated 21 GGAAAUCAUUCCAUUCAAUGAUGUUCAAUGAAACA DNA pool, Aggregated Drop UCAUUUGAAUGGAAUUGAUUGG (SEQ ID NO: 113) Reaction, 1 day time point Seeded with DNase-treated 22 GGAAAAAUAAUGGGAUACUUCAAACAUUAUUUUUC DNA pool, Aggregated Drop CGAAAAAUAAUGUUUGAAGUAUCCCAUUAUUUUU Reaction, 1 day time point GG (SEQ ID NO: 114) Seeded with DNase-treated 23 GGGAAAAUCAAUUCCAGUCCUUUCCCUGGAUUUG DNA pool, Aggregated Drop AAAAUCAAUUCCAGGGAAAGGACUGGAAUUGAUU Reaction, 1 day time point UUGG (SEQ ID NO: 115) Seeded with DNase-treated 24 GGAAGAAAAUCAAAUAAUAUAUCUGGAUACAUUAU DNA pool, Aggregated Drop UUGAUUUUCAAAUAAUGUAUCCAGAUAUAUUAUUU Reaction, 1 day time point GAUUUUCUUGG (SEQ ID NO: 116) Seeded with DNase-treated 25 GGAAAAUUUGAUACUAGCUAUCCAAAGUAUCAAAU DNA pool, Aggregated Drop UUCAUGAUACUUUGGAUAGCUAGUAUCAAAUUUG Reaction, 1 day time point GG (SEQ ID NO: 117) Seeded with DNase-treated 26 GGAAAUAAAAUCAUCAUUAUUAUUUGAUGAAAUAA DNA pool, Aggregated Drop AAUCAUCAAAUAAUAAUGAUGAUUUUAUUUGG Reaction, 1 day time point (SEQ ID NO: 118) Seeded with DNase-treated 27 GGAAAAUUAAAUUGCAUUGAACUUUAAUUUUCCCC DNA pool, Aggregated Drop CCAAAAUUAAAGUUCAAUGCAAUUUAAUUUUGG Reaction, 1 day time point (SEQ ID NO: 119) Seeded with DNase-treated 28 GGAAGAUGUUUUUGAUACCGAGCUGGUCUCAGCA DNA pool, Aggregated Drop UAUAUUUCCAUAAAUAUAUGCUGAGACCAGCUCG Reaction, 1 day time point GUAUCAAAACAUCUAUGG (SEQ ID NO: 120) Seeded with DNase-treated 29 GGAUGAAAUUGGAAACCAUCAUUCUCCCCAAAUU DNA pool, Aggregated Drop UCAUCCAAUGAAAUUGGGAGAAUGAUGGUUUCCA Reaction, 1 day time point AUUUCUUGG (SEQ ID NO: 121) Seeded with DNase-treated 30 GGAAAAUUAUAAUAGAAAUUAUCCCUAUUAUAAUU DNA pool, Aggregated Drop AUAAUAGGGAUAAUUUCUAUUAUAAUUUUGG Reaction, 1 day time point (SEQ ID NO: 122) Seeded with DNase-treated 31 GGAUGAAAUCAAAAAAGCUAGUCCUUUUGAUGAAA DNA pool, Aggregated Drop AUCAAAAGGACUAGCUUUUGAUUUCAUGG Reaction, 1 day time point (SEQ ID NO: 123) Seeded with DNase-treated 32 GGAAUUAAACAAAUAUAUACUUCCACAAUAUUUGU DNA pool, Aggregated Drop UUGAAAACAAAUAUUGUGGAAGUAUAUAUUUGUU Reaction, 1 day time point UUCGG (SEQ ID NO: 124) Seeded with DNase-treated 33 GGAUUUUUGAUUUCAUUCGAUGCUUCUGAAAAUC DNA pool, Aggregated Drop AAUAAUUCCCAUUUGAUUUUCAGAAGCAUCGAAU Reaction, 1 day time point GAAAUCAAAUGG (SEQ ID NO: 125) Seeded with DNase-treated 34 GGAUAAAAUUCUAGUCUAUAUGGCUACUAGAAUA DNA pool, Aggregated Drop CUAAAUUCUAGUAGCCAUAUAGACUAGAAUUUAUG Reaction, 1 day time point G (SEQ ID NO: 126) Seeded with DNase-treated 35 GGAAUUGAAAUUCAUCUUCUGUCUCUUGUGAAUU DNA pool, Aggregated Drop UCAUUUUAAUUGAUUGAAAUUCACAAGAGACAGAA Reaction, 1 day time point GAUGAAUUUCAAUCAUGG (SEQ ID NO: 127) Seeded with DNase-treated 36 GGAAAUUUCAUAUUUCAGAAAUAGGUAAAUUUCU DNA pool, Aggregated Drop GAAAUAAAAUAAAUUUUUUAUUUCAGAAAUUUACC Reaction, 1 day time point UAUUUCUGAAAUAUGAAAUUUGG (SEQ ID NO: 128) Seeded with DNase-treated 37 GGAAUUAUGAUCAAAAUUGAAUGGAAAUUGAAUGA DNA pool, Aggregated Drop UCAAAUUGAAUUAUGAUCAUUCAAUUUCCAUUCAA Reaction, 1 day time point UUUUGAUCAUAAUUGG (SEQ ID NO: 129) Seeded with DNase-treated 38 GGAAGAAAAUGUUAUCUACACCGAGACAUAACAUU DNA pool, Aggregated Drop UUCUGACAGAAAUGUUAUGUCUCGGUGUAGAUAA Reaction, 1 day time point CAUUUCUUGG (SEQ ID NO: 130) Seeded with DNase-treated 39 GGAUUAAAUUUCAAAUUAUUCCCUAAUAAUUUGAA DNA pool, Aggregated Drop AAUUUCAAAUUAUUAGGGAAUAAUUUGAAAUUUUG Reaction, 1 day time point G (SEQ ID NO: 131) Seeded with DNase-treated 40 GGAAUGUUUAUUCUUUAUUCAAAUAAGGUUUUAA DNA pool, Aggregated Drop AGAAUAAACUGAAUAAAAUUUAUUCUUUAUUCAGU Reaction, 1 day time point UUAUUCUUUAAAACCUUAUUUGAAUAAAGAAUAAA CUGG (SEQ ID NO: 132) Seeded with DNase-treated 41 GGGGGAAAAUUUCAAGAUCAGGGCUUGAAAUUUU DNA pool, Aggregated Drop UACAAAAUUUCAAGCCCUGAUCUUGAAAUUUUGG Reaction, 1 day time point G (SEQ ID NO: 133) Seeded with DNase-treated 42 GGAUAAAAUAUCGUAUUUUUCCUCUAAUGUGGAU DNA pool, Aggregated Drop AUUUUAUGGCCAUAAAAUAUCCACAUUAGAGGAAA Reaction, 1 day time point AAUACGAUAUUUUAUGG (SEQ ID NO: 134) Seeded with DNase-treated 43 GGAAUUAAUUAAUAUCUCUAAAUUAUUAAUUCGAG DNA pool, Aggregated Drop AAUUAAUAAUUUAGAGAUAUUAAUUCGG Reaction, 1 day time point (SEQ ID NO: 135) Seeded with DNase-treated 44 GGGGAAAUUUUCAAGUUAUUUCUUUACUUGAAAU DNA pool, Aggregated Drop UUUCAAGUAAAGAAAUAACUUGAAAAUUUGG Reaction, 1 day time point (SEQ ID NO: 136) Seeded with DNase-treated 45 GGAUUAUGAAAUUUACAUUGCUUCAAUUCAUAAUC DNA pool, Aggregated Drop UCCAUUAUGAAUUGAAGCAAUGUAAAUUUCAUAAU Reaction, 1 day time point GGG (SEQ ID NO: 137) Seeded with DNase-treated 46 GGGAAUUUUAAUUUCAUAUUAUCGAUGAAUGAAA DNA pool, Aggregated Drop UUAUUGAAUUUAAUUUCAUUCAUCGAUAAUAUGAA Reaction, 1 day time point AUUAAAUUGG (SEQ ID NO: 138) Seeded with DNase-treated 47 GGAAAAUCUUGUCAUGAAUCAAUAGAUUUUCUUG DNA pool, Aggregated Drop UCAUGAAAUCUAUUGAUUCAUGACAAGAUUUUGG Reaction, 1 day time point (SEQ ID NO: 139) Seeded with DNase-treated 48 GGAAAAACAAUCUACAAAUUCAAUGCCGAAUUGAA DNA pool, Aggregated Drop UUUGUUGAUCUACAAAUUUAAUUCGGCAUUGAAU Reaction, 1 day time point UUGUAGAUUGUUUUUUGGG (SEQ ID NO: 140) Seeded with DNase-treated 49 GGAAAAUCAAGAUAAUAAAUACUCCAUUAUUAUCU DNA pool, Aggregated Drop CAGAUAAUAAUGAUGGAGUAUUUAUUAUCUUGAU Reaction, 1 day time point UUGG (SEQ ID NO: 141) Seeded with DNase-treated 50 GGAAAAUUUCUAAAUUGAAAGAUAAAAUUUAAUUU DNA pool, Aggregated Drop UCUAAAUUUUAUCUUUCAAUUUAGAAAUUUUGG Reaction, 1 day time point (SEQ ID NO: 142) Seeded with DNase-treated 51 GGGAAAAAAUAUUUUCUAAAUGGUGAGAAAUAUUU DNA pool, Aggregated Drop UCCGAAAAUAUUUCUCACCAUUUAGAAAAUAUUUC Reaction, 1 day time point GG (SEQ ID NO: 143) Seeded with DNase-treated 52 GGAAUUAUUUUCAUUUGUGUACUCAGUACACGAA DNA pool, Aggregated Drop UUUAAUUAUUUUCCAAAAUUCGUGUACUGAGUAC Reaction, 1 day time point ACAAAUGAAAAUAAUUGG (SEQ ID NO: 144) Seeded with DNase-treated 53 GGAUAAUUAUCAAUAAUUCGAAUAAUUAUCAAUAA DNA pool, Aggregated Drop UUAUUCGAAUUAUUGAUAAUUAUGGG Reaction, 1 day time point (SEQ ID NO: 145) Seeded with DNase-treated 54 GGAUAAUUUCAUUUAUAAUGAAGUUAUUCAUUUAU DNA pool, Aggregated Drop AAUGAAUAACUUCAUUAUAAAUGAAAUUCGGGG Reaction, 1 day time point (SEQ ID NO: 146) Seeded with hot alkali- 1 GGAAAUAAUCAUAUUCUCAUAAUGAGAUUAUUAAA treated DNA pool, UUUCCAUUAAUAAUCUCAUUAUGAGAAUAUGAUUA Aggregated Drop Reaction, AUGG (SEQ ID NO: 147) 1 day time point Seeded with hot alkali- 2 GGAUAAAUUUGUGUCUUCUAUUCUUAACAAAUUU treated DNA pool, GUUUUCCAUAAUUUGUUAAGAAUAGAAGACACAAA Aggregated Drop Reaction, UUAUGG (SEQ ID NO: 148) 1 day time point Seeded with hot alkali- 3 GGAAUAAUUCAAUUAUUAUUGAUAAUAAUUCAAUU treated DNA pool, AUUAUCAAUAAUAAUUGAAUUAUUGG Aggregated Drop Reaction, (SEQ ID NO: 149) 1 day time point Seeded with hot alkali- 4 GGAAUAUAUUAUAUGAAAUCUCUUCGUCUCAUAUA treated DNA pool, AUAUAUAUAUGGAGACGAAGAGAUUUCAUAUAAUA Aggregated Drop Reaction, UAUAUGG (SEQ ID NO: 150) 1 day time point Seeded with hot alkali- 5 GGAAAUUUGAAUCAAUUCCUCCAAAUUGGUUCAAA treated DNA pool, UCUCAAUUUGAUGAAUUGAUUCAUCAAAUUGAUU Aggregated Drop Reaction, UGAAUCAAUUUGGAGGAAUUGAUUCAAAUUUGG 1 day time point (SEQ ID NO: 151) Seeded with hot alkali- 6 GGAAAAAUUGUUCUCUAAUUGAUUCAUUCCGAAC treated DNA pool, AAUUUUGAUCCAAAAUUGUUCGGAAUGAAUCAAUU Aggregated Drop Reaction, AGAGAACAAUUUUGG (SEQ ID NO: 152) 1 day time point Seeded with hot alkali- 7 GGGAAUAUUCUAUUCUUGCUCUUCUAGAGAGAGA treated DNA pool, AUAUUCUACUCUCUCUCUAGAAGAGCAAGAAUAGA Aggregated Drop Reaction, AUAUUGG (SEQ ID NO: 153) 1 day time point Seeded with hot alkali- 8 GGAUAAUUAAUUAUUACUCUCAUUGGAUGUUGGG treated DNA pool, UAAAAAAUUAAUUAUUACCCAACAUCCAAUGAGAG Aggregated Drop Reaction, UAAUAAUUAAUUUGG (SEQ ID NO: 154) 1 day time point Seeded with hot alkali- 9 GGAAAAAUCAACAGAUACAAAUUGAUUGAUUUUCC treated DNA pool, AAAUCCAAAAAUCAAUCAAUUUGUAUCUGUUGAUU Aggregated Drop Reaction, UUGGG (SEQ ID NO: 155) 1 day time point Seeded with hot alkali- 10 GGAAUAUUUCAAUAUUUCAAAGAAAGGAAAAUAUU treated DNA pool, GAUAUUUCAAUAUUUUCCUUUCUUUGAAAUAUUG Aggregated Drop Reaction, AAAUAUUGG (SEQ ID NO: 156) 1 day time point Seeded with hot alkali- 11 GGAAAAAAAUUCAUUCGAAGUACUUUGAAUUUUU treated DNA pool, GUUUUCCAAAAUUCAAAGUACUUCGAAUGAAUUUU Aggregated Drop Reaction, GG (SEQ ID NO: 157) 1 day time point Seeded with hot alkali- 12 GGAAUAAUAUUCUAUCCUUCGAGAAUAUUAGUCU treated DNA pool, AUAAUAUUCUCGAAGGAUAGAAUAUUAUAGGGG Aggregated Drop Reaction, (SEQ ID NO: 158) 1 day time point Seeded with hot alkali- 13 GGAUUUAAUCUUCAUAGAAAUAGUAUAAGAUUAAU treated DNA pool, CACAUUAAUCUUAUACUAUUUCUAUGAAGAUUAAU Aggregated Drop Reaction, GG (SEQ ID NO: 159) 1 day time point Seeded with hot alkali- 14 GGAGAAUUUCUAAAUAGAUUACAUUUCAUUGUAAU treated DNA pool, GUAAUCUACAAUUUCAUUGUAGAUUACAUUACAAU Aggregated Drop Reaction, GAAAUGUAAUCUAUUUAGAAAUUCUGG 1 day time point (SEQ ID NO: 160) Seeded with hot alkali- 15 GGAAAAUUUGUAAUUCAAAUUGGUAACAAAUUUGU treated DNA pool, AAUUCAAAUUUGUUACCAAUUUGAAUUACAAAUUU Aggregated Drop Reaction, UGGG (SEQ ID NO: 161) 1 day time point Seeded with hot alkali- 16 GGAAAAUUUCAAUAACAAAAAAUCCCGUUAUUGAA treated DNA pool, AAAUUUUCAAUAACGGGAUUUUUGUUAUUGAAAU Aggregated Drop Reaction, UUUGG (SEQ ID NO: 162) 1 day time point Seeded with hot alkali- 17 GGAAAAUUCAAUUGCUGGAAAAAUUGAAUUGUUC treated DNA pool, CAAAUUCAAUUUCCAGCAAUUGAAUUUUGGG Aggregated Drop Reaction, (SEQ ID NO: 163) 1 day time point Seeded with hot alkali- 18 GGGGAAGAAGUUCUCAAUGUAGAUAUUAUGUGCA treated DNA pool, UUGAAGAAGUUCUAAAUGCACAUAAUAUCUACAUU Aggregated Drop Reaction, GAGAACUUCUUGGG (SEQ ID NO: 164) 1 day time point Seeded with hot alkali- 19 GGAAAAAUAUCAAAAUACACCCUUAUUUUGAUAUA treated DNA pool, AAAUAUCAAAAAUAAGGGUGUAUUUUGAUAUUUUA Aggregated Drop Reaction, UGG (SEQ ID NO: 165) 1 day time point Seeded with hot alkali- 20 GGAAAAAUUGAAUUUAUUGAAUGUUUUGGUCAUU treated DNA pool, CAAUUUUUCCGAAAAAUUGAAUGACCAAAACAUUC Aggregated Drop Reaction, AAUAAAUUCAAUUUUUGG (SEQ ID NO: 166) 1 day time point Seeded with hot alkali- 21 GGGAUUUUUCAAUCAAAUGACGAGAGAUUGAAAU treated DNA pool, UGCCAAUUUCAAUCUCUCGUCAUUUGAUUGAAAU Aggregated Drop Reaction, UGG (SEQ ID NO: 167) 1 day time point Seeded with hot alkali- 22 GGAUUUAUAAUCAUCGAUCAUAAUAUUAUAAUCGA treated DNA pool, UCAAUUAUAAUAUUAUGAUCGAUGAUUAUAAUUGG Aggregated Drop Reaction, (SEQ ID NO: 168) 1 day time point Seeded with hot alkali- 23 GGAAAAUAUUUUACAUCUGGAAUUAAAAUAUUUUU treated DNA pool, CUCCAAAUAUUUUAAUUCCAGAUGUAAAAUAUUUG Aggregated Drop Reaction, G (SEQ ID NO: 169) 1 day time point Seeded with hot alkali- 24 GGGAAAAAAAUCUAAUUGAUCAGAGACAAUUAGAU treated DNA pool, UAGAAAAUCUAAUUGUCUCUGAUCAAUUAGAUUUU Aggregated Drop Reaction, UGG (SEQ ID NO: 170) 1 day time point Seeded with hot alkali- 25 GGAUUAUUAUUAUUUGAAUCAAUUCCCAAAUAAUA treated DNA pool, AUCAAAUUAUUAUUUGGGAAUUGAUUCAAAUAAUA Aggregated Drop Reaction, AUUGG (SEQ ID NO: 171) 1 day time point Seeded with hot alkali- 26 GGAAAAAAUUUCAUAUUUUCAAUUCCAAUAUGAAA treated DNA pool, AUUUCAUAUUGGAAUUGAAAAUAUGAAAUUUUCG Aggregated Drop Reaction, G (SEQ ID NO: 172) 1 day time point Seeded with hot alkali- 27 GGAUAAAAUCUUAUAUCUUUCAUCUAGAGAUAUGA treated DNA pool, UGAUUUAUAUCUUUCAUCAUAUCUCUAGAUGAAA Aggregated Drop Reaction, GAUAUAAGAUUUUUUUGG (SEQ ID NO: 173) 1 day time point Seeded with hot alkali- 28 GGAAAAAUAAAUUUGUUCCAUUUCACAAAUUUAUU treated DNA pool, CCGAAUAAAUUUGUGAAAUGGAACAAAUUUAUUUU Aggregated Drop Reaction, GGG (SEQ ID NO: 174) 1 day time point Seeded with hot alkali- 29 GGUUUAAUUUUAACAUUUUGGGUGUGUUAAUUUU treated DNA pool, AACACACCCAAAAUGUUAAAAUUAAUGG Aggregated Drop Reaction, (SEQ ID NO: 175) 1 day time point Seeded with hot alkali- 30 GGAAAUAUAAUAUAAGUUUGGUAUUCCUUAUAUUA treated DNA pool, UAUAUUUAUAUAAUAUAAGUGAAUACCAAACUUAU Aggregated Drop Reaction, AUUAUAUUGGG (SEQ ID NO: 176) 1 day time point Seeded with hot alkali- 31 GGAUUAUUUCAAUGUUUCACUAAUUCAUUGAAUU treated DNA pool, AUUUCAAUGAAUUAGUGAAACAUUGAAAUAAUGGG Aggregated Drop Reaction, GGG (SEQ ID NO: 177) 1 day time point Seeded with hot alkali- 32 GGAAUAAUUGAAUAAUUAGACUUAUCCAAUUUUCC treated DNA pool, AAAAUUGGAAAAUUGGAUAAGUCUAAUUAUUCAAU Aggregated Drop Reaction, UUUGG (SEQ ID NO: 178) 1 day time point Seeded with hot alkali- 33 GGAUAAUUAAUCAAAUGAAUACAUGAUUAAUUAAA treated DNA pool, AUGAUUUAAUUAAUCAUGUAUUCAUUUGAUUAAUU Aggregated Drop Reaction, AAUGG (SEQ ID NO: 179) 1 day time point Seeded with hot alkali- 34 GGAAAUUUUCAAUUUCACAUCAUGAUCCGUGUUU treated DNA pool, UGAAUUUUCAAUUUCACACGGAUCAUGAUGUGAA Aggregated Drop Reaction, AUUGAAAAUUUAGG (SEQ ID NO: 180) 1 day time point Seeded with hot alkali- 35 GGAAAAAUCAAUUCAUUUGAAGAGUUCCAAAAUCA treated DNA pool, AUUCUCUUCAAAUUCAUUGAAGAGAAUUGAUUUU Aggregated Drop Reaction, UUGGAACUCUUCAAAUGAAUUGAUUUUGGG 1 day time point (SEQ ID NO: 181) Seeded with hot alkali- 36 GGAAAAUUAUAUCAAGUAACACAACCAGAUAUAUU treated DNA pool, UUUUUCUAUAUCUGGUUGUGUUACUUGAUAUAAU Aggregated Drop Reaction, UUUGGG (SEQ ID NO: 182) 1 day time point Seeded with hot alkali- 37 GGAAUGAAAAUUGUUUGAUAAGAAAGGAUAAGCAA treated DNA pool, CAAUUUUCUGAAAAUUGUUGCUUAUCCUUUCUUA Aggregated Drop Reaction, UCAAACAAUUUUCUUGG (SEQ ID NO: 183) 1 day time point Seeded with hot alkali- 38 GGAAAAUUGAAAUGAAAAAAUUCCAUUUCAUUUCA treated DNA pool, UUUCAAAAAAUUGAAAUGAAAUGAAAUGGAAUUUU Aggregated Drop Reaction, UCAUUUCAAUUUUGG (SEQ ID NO: 184) 1 day time point Seeded with hot alkali- 39 GGAAAUAUACAAUUCUAUAUCAUUCAGAUAUAGAA treated DNA pool, UGAAAUUGCCAAAUUUCCUUCUAUAUCUGAAUGA Aggregated Drop Reaction, UAUAGAAUUGUAUAUUUGG (SEQ ID NO: 185) 1 day time point Seeded with hot alkali- 40 GGAAAUUAAUUCAAUUAUCAUCAAUUAAUUUGGAU treated DNA pool, GAUUCCAAAUUAAUUGAUGAUAAUUGAAUUAAUUU Aggregated Drop Reaction, GG (SEQ ID NO: 186) 1 day time point Seeded with hot alkali- 41 GGAAAAUUUCAAUCAAUUCCAUUCCUGAUUGAAAA treated DNA pool, UUUCAAUCAGGAAUGGAAUUGAUUGAAAUUUUGG Aggregated Drop Reaction, GGGGG (SEQ ID NO: 187) 1 day time point Seeded with hot alkali- 42 GGAAAAAAAUAUAAUAUGUCAUUUCCAUAUUAUAU treated DNA pool, AUAAUAAUAUGGAAAUGACAUAUUAUAUUUUGGG Aggregated Drop Reaction, (SEQ ID NO: 188) 1 day time point Unseeded, Aggregated 1 GGAUUAAUCAAAUCCUCAAUAUUUUGAUUAAUUAA Drop Reaction, 5 day time UAUUGAAUUAAUUAAUCAAAAUAUUGAGGAUUUGA point UUAAUUAAUUCGG (SEQ ID NO: 189) Unseeded, Aggregated 2 GGAAAUUAGAAUCAAACGUCUCAAUUCUAAUUCCG Drop Reaction, 5 day time AAAUUAGAAUUGAGACGUUUGAUUCUAAUUUGGG point (SEQ ID NO: 190) Unseeded, Aggregated 3 GGAUUAUUAGAAGACAAUUAAACUAAUAAUAAUCC Drop Reaction, 5 day time CUUUAUUAUUAGUUUAAUUGUCUUCUAAUAAAGG point (SEQ ID NO: 191) Unseeded, Aggregated 4 GGAAAAUAUUUGAAUUGCAAUUCCCAAAUAUUUG Drop Reaction, 5 day time GCCAAAUAUUUGGGAAUUGCAAUUCAAAUAUUUG point G (SEQ ID NO: 192) Unseeded, Aggregated 5 GGAAUUUAAAUCAAAGUUCUUAUUAAAUUGCUUU Drop Reaction, 5 day time GAAUUUAAAUCAAAGCAAUUUAAUAAGAACUUUGA point UUUAAAUUGG (SEQ ID NO: 193) Unseeded, Aggregated 6 GGAUAUUUAUCAUCGAGGUGUUGAGAGAUAAAAU Drop Reaction, 5 day time CCAUUAUUUAUCUCUCAACACCUCGAUGAUAAAUA point AUGG (SEQ ID NO: 194) Unseeded, Aggregated 7 GGAAUAUUCAAUUAAUAUUGAAACAAAAUUAAUUG Drop Reaction, 5 day time AUUUAAUUCAAUUAAUUUUGUUUCAAUAUUAAUUG point AAUAUGG (SEQ ID NO: 195) Unseeded, Aggregated 8 GGAUAUAUUUCAAUAUAUGGUAGAUAUAUUUCAAU Drop Reaction, 5 day time AUAUCUACCAUAUAUUGAAAUAUAGG point (SEQ ID NO: 196) Unseeded, Aggregated 9 GGAAGAAUUUGUUAUUUUGCUUCUUAACACAAAU Drop Reaction, 5 day time UCUUCCGAAGAAUUUGUGUUAAGAAGCAAAAUAAC point AAAUUCUUGG (SEQ ID NO: 197) Unseeded, Aggregated 10 GGAUGAAUUAGAGUCUACCUGUUAACCUCCUCUA Drop Reaction, 5 day time AUUCUACUGAAUUAGAGGUUAACAGGUAGACUCU point AAUUCAGG (SEQ ID NO: 198) Unseeded, Aggregated 11 GGAAAAUUUCAAAUUUCUUCACAUUUGAAAUUUCA Drop Reaction, 5 day time AAUUUCAAAUGUGAAGAAAUUUGAAAUUUGGG point (SEQ ID NO: 199) Unseeded, Aggregated 12 GGAUUUCAUAAACAAAUUCGAAUGUUUAUGAAAUC Drop Reaction, 5 day time UAAGAAAUAGAUUUCAUAAACAUUCGAAUUUGUUU point AUUCUGG (SEQ ID NO: 200) Unseeded, Aggregated 13 GGAUGAAUUUGAUUUAGAUUUGGCAUUUAUCAAA Drop Reaction, 5 day time UUCAUCCGAUGAAUUUGAUAAAUGCCAAAUCUAAA point UCAAAUUCAUGG (SEQ ID NO: 201) Unseeded, Aggregated 14 GGAAACAUUGAUUAAUAAUACGUUCAAUUUAUCAA Drop Reaction, 5 day time AUGUUUUCCGAAAAACAUUGAUAAAUUGAACGUAU point UAUUAAUCAAUGUUUGG (SEQ ID NO: 202) Unseeded, Aggregated 15 GGAUAAAAAGAAUUGUUCCUUUCUCUUCUUUUUA Drop Reaction, 5 day time UGUUCCAUAAAAGAAGAGAAAGGAACAAUUCUUUU point AUGG (SEQ ID NO: 203) Unseeded, Aggregated 16 GGAAAAAUACAAGUUUCCUAUAUUCAUUGUAUUUU Drop Reaction, 5 day time CUCCAAAAUACAAUGAAUAUAGGAAACUUGUAUUU point UGG (SEQ ID NO: 204) Unseeded, Aggregated 17 GGAAAAUAUUGAAUCUACCGAUGUCUCAAUAUUU Drop Reaction, 5 day time CCGAAAUAUUGAGACAUCGGUAGAUUCAAUAUUU point UGG (SEQ ID NO: 205) Unseeded, Aggregated 18 GGAAGAAACAAUAAUUUUUCCCUGUUCUUUAUUG Drop Reaction, 5 day time UUUCCCGAAACAAUAAAGAACAGGGAAAAUUAUUG point UUUCUUGG (SEQ ID NO: 206) Unseeded, Aggregated 19 GGAAAAUUGAAAUUUCGGAAAUUUUCAAUUUUGG Drop Reaction, 5 day time ACCAAAAUUGAAAAUUUCCGAAAUUUCAAUUUGG point (SEQ ID NO: 207) Unseeded, Aggregated 20 GGAAUAUUGAAUAUGAAUAUCCAUAUUCAUGAUUC Drop Reaction, 5 day time AUGAAUAUGGAUAUUCAUAUUCAAUAUGGG point (SEQ ID NO: 208) Unseeded, Aggregated 21 GGAAAUUAUCAAUGUGUGGUAUGGAUCAACAUUG Drop Reaction, 5 day time AAAUUAUCAAUGUUGAUCCAUACCACACAUUGAUA point AUUUGG (SEQ ID NO: 209) Unseeded, Aggregated 22 GGAAUUUUGGAAUUUGACAACUGGUAUCCAAAAU Drop Reaction, 5 day time UCCGAAUUUUGGAUACCAGUUGUCAAAUUCCAAA point AUUGG (SEQ ID NO: 210) Unseeded, Aggregated 23 GGAAAAAUUGCUAAUAUCAUCUUGAAAGCAAUUUU Drop Reaction, 5 day time CCCAAAUUGCUUUCAAGAUGAUAUUAGCAAUUUU point GG (SEQ ID NO: 211) Unseeded, Aggregated 24 GGAUAAUAAUCAUUAUUAUUCCCUAUAAAAUAAUG Drop Reaction, 5 day time AUUUAUGAAAUAAUCAUUAUUUUAUAGGGAAUAAU point AAUGAUUAUUCGG (SEQ ID NO: 212) Unseeded, Aggregated 25 GGAAAAUUGCAAUUAUUUCCUUCCAUUGCAAUUA Drop Reaction, 5 day time UUUCCAAAUUGCAAUGGAAGGAAAUAAUUGCAAUU point UUGG (SEQ ID NO: 213) Unseeded, Aggregated 26 GGAAAUACAUUUUCAUCCAAAAAAUGUAUUUUUCA Drop Reaction, 5 day time UCCAAAAAUACAUUUUUUGGAUGAAAAUGUAUUUG point G (SEQ ID NO: 214) Unseeded, Aggregated 27 GGAAAAUUAUUCAAAUAAAUAAUUGGAAUUAUUCA Drop Reaction, 5 day time AAUUAUUCCAAUUAUUUAUUUGAAUAAUUUGG point (SEQ ID NO: 215) Unseeded, Aggregated 28 GGAAAUAAUUCAAUUAUUUAUUUAAUUGAAUAAUU Drop Reaction, 5 day time CAAUUAAAUAAAUAAUUGAAUUAUUUGG point (SEQ ID NO: 216) Unseeded, Aggregated 29 GGAAUAAUUAAUCAACAUCAUGAUUAUUAAUUAAU Drop Reaction, 5 day time CCAAUAAUUAAUAAUCAUGAUGUUGAUUAAUUAUU point GG (SEQ ID NO: 217) Unseeded, Aggregated 30 GGAUAAUCAUUUAUUUAUGUCUUCCCCAAUAAAAU Drop Reaction, 5 day time AAAUGAUUAUCCAAUCAUUUAUUUUAUUGGGGAA point GACAUAAAUAAAUGAUAUGG (SEQ ID NO: 218) Unseeded, Aggregated 31 GGAAAAUUAAUAAUCCUAAAUUCCAGGGGAUUAUU Drop Reaction, 5 day time UUAGAAAUUAAUAAUCCCCUGGAAUUUAGGAUUAU point UAAUUUCGG (SEQ ID NO: 219) Unseeded, Aggregated 32 GGAAAAAAAUCAAAGAGAGCUUUUCUUUGAAUCAA Drop Reaction, 5 day time AGAAUCAAAGAAAAGCUCUCUUUUGAUUUGG point (SEQ ID NO: 220) Unseeded, Aggregated 33 GGAAAAUUCAACAAAUUCUUCAAUUUCAAAUGUUG Drop Reaction, 5 day time AAUUUCAACAAAUUCAACAUUUGAAAUUGAAGAAU point UUGUUGAAUUUUGG (SEQ ID NO: 221) Unseeded, Aggregated 34 GGAAAAAUAAAGAUGUAGCUAAACGCUAUAUAUUC Drop Reaction, 5 day time CCAAUAUAUAGCGUUUAGCUACAUCUUUAUUUUU point GG (SEQ ID NO: 222) Unseeded, Aggregated 35 GGAAUAAUAAUCAUUGAACGGAAUCCUCAAUGAUU Drop Reaction, 5 day time AUUUCAUUUAAUCAUUGAGGAUUCCGUUCAAUGA point UUAUUCGG (SEQ ID NO: 223) Unseeded, Aggregated 36 GGAAAAUAAUUUCUAUUAAAUUAUUUGAUAGAAAU Drop Reaction, 5 day time AAUUUCUAUCAAAUAAUUUAAUAGAAAUUAUUUUG point G (SEQ ID NO: 224) Unseeded, Aggregated 37 GGAUAAUAUUUCUAAUUAACUACCCAUAAUUAGAA Drop Reaction, 5 day time AUAUUUCUAAUUAUGGGUAGUUAAUUAGAAAUAUU point CGG (SEQ ID NO: 225) Unseeded, Aggregated 38 GGAAAAAUUCAAUAAUCUCUAUUAUUAUUGAAAAA Drop Reaction, 5 day time UUCAAUAAUAAUAGAGAUUAUUGAAUUUUUGG point (SEQ ID NO: 226) Unseeded, Aggregated 39 GGAAAAAUUCAAAAUUGUUGUCUGAAUUGAAUUAU Drop Reaction, 5 day time UUUCCCAAAAUUCAAUUCAGACAACAAUUUUGAAU point UUUGGG (SEQ ID NO: 227) Unseeded, Aggregated 40 GGAUGAUCAAUGUGUCCUGCAAUUCACACACAUU Drop Reaction, 5 day time GACAUGAUCAAUGUGUGAAUUGCAGGACACAUUG point AUCUUGG (SEQ ID NO: 228) Unseeded, Aggregated 41 GGAAAUAUUAUAAAUACAUAUGGGAGAAGUUGUA Drop Reaction, 5 day time UUAUAAAUACAACUUCUCCCAUAUGUAUUUAUAAU point AUUUGG (SEQ ID NO: 229) Unseeded, Aggregated 42 GGAAAAAUUGGAUUCAUAACUUCGCCUAUCCAAU Drop Reaction, 5 day time UUUCCCGAAAAUUGGAUAGGCGAAGUUAUGAAUC point CAAUUUUGGG (SEQ ID NO: 230) Unseeded, Aggregated 43 GGAAAAAAAUUCAUUCGAAUGAAAUUGAUUUCAUU Drop Reaction, 5 day time CGAAUGAAAUCAAUUUCAUUCGAAUGAAUUUUUUU point GG (SEQ ID NO: 231) Unseeded, Aggregated 44 GGAAAAUCAAAUACUUGGUCUAUUUUAUUUGAUU Drop Reaction, 5 day time UUCUCAAAAUAAAAUAGACCAAGUAUUUGAUUUUG point G (SEQ ID NO: 232) Unseeded, Aggregated 45 GGAAUAAUUUCAAACAUCAUUGUCCUUUGUUUGA Drop Reaction, 5 day time AUAAUUUCAAACAAAGGACAAUGAUGUUUGAAAUU point AUUGG (SEQ ID NO: 233) Unseeded, Aggregated 46 GGAAUUUAUUCAAUUCAUCUGCAAUUGAAUUAAUU Drop Reaction, 5 day time UAUUCAAUUGCAGAUGAAUUGAAUAAAUUAGG point (SEQ ID NO: 234) Unseeded, Aggregated 47 GGAUUCAAUUAGGUAUUCAAUCUUCCCCUAAUUG Drop Reaction, 5 day time AAUCUCAAUUAGGGGAAGAUUGAAUACCUAAUUU point CUGG (SEQ ID NO: 235) Unseeded, Aggregated 48 GGAAUAUCAAAUUUCCAAUAUGUUUUGAUUUCCAA Drop Reaction, 5 day time AUAUCAAAAACAUAUUGGAAAUUUGAUAUUGG point (SEQ ID NO: 236) Unseeded, Aggregated 49 GGAAAAUUCCAAUUUUGGUCGAUGGAAACAAAAU Drop Reaction, 5 day time UGGAAUUCCAAUUUUGUUUCCAUCGACCAAAAUU point GGAAUUUGGG (SEQ ID NO: 237) Unseeded, Aggregated 50 GGAAAAUAUUUCUCAUAUUGGGCGAUAUUUCUCA Drop Reaction, 5 day time AUAUCGCCCAAUAUGAGAAAUAUUUUGGG point (SEQ ID NO: 238) Unseeded, Aggregated 51 GGAAAAAAAUUAUCAUUGGUGUGGGAUGAUAAUU Drop Reaction, 5 day time UCUCGAAAUUAUCAUCCCACACCAAUGAUAAUUUU point CGG (SEQ ID NO: 239) Unseeded, Aggregated 52 GGAAAAAUUCAAAUUCAAUCGAGAAUAAUUUGAAU Drop Reaction, 5 day time CAAAAUUCAAAUUAUUCUCGAUUGAAUUUGAAUUU point UGG (SEQ ID NO: 240) Unseeded, Aggregated 53 GGAUUAUUGAUUUCCAUCAACAUCAAUAAUCGCUA Drop Reaction, 5 day time UUAUUGAUGUUGAUGGAAAUCAAUAAUAGGG point (SEQ ID NO: 241) Unseeded, Aggregated 54 GGAUUAAUAAUCAUUUCGAAAUGAUUUCCAAUAAA Drop Reaction, 5 day time CGAAAUGAUUAUUGGAAAUCAUUUCGAAAUGAUUA point UUGG (SEQ ID NO: 242) Unseeded, Aggregated 55 GGAAUUGAAUUCAAAAUCUCAAUUGAUUUCAUUCC Drop Reaction, 5 day time AAUUGAAAAUCAAUUGAGAUUUUGAAUUCAAUUGG point (SEQ ID NO: 243) Unseeded, Aggregated 56 GGGAAAAUUCAAAAGUUUCCUGAACUUUUUUGAA Drop Reaction, 5 day time AAUUCAAAAGUUCAGGAAACUUUUGAAUUUUGGG point (SEQ ID NO: 244) Unseeded, Aggregated 57 GGAUCAUUAAUAUCAUUACUACAGUCUAGUAAUGA Drop Reaction, 5 day time UAUCAUUACUAGACUGUAGUAAUGAUAUUAAUCU point GG (SEQ ID NO: 245) Unseeded, Aggregated 58 GGAAAAUAAUUCUAAUAUUUGCAUUUAUUUUAGAA Drop Reaction, 5 day time AAUAAUUCUAAUAUUUUCUAAAAUAAAUGCAAAUA point UUAGAAUUAUUUGG (SEQ ID NO: 246) Unseeded, Aggregated 59 GGAUGAAAUCUUCAUAAUAUUAUCGUAUAUAUAUU Drop Reaction, 5 day time UCAUAAUAUAUAUACGAUAAUAUUAUGAAGAUUGG point G (SEQ ID NO: 247) Unseeded, Aggregated 60 GGGAAUAAUUAAUUGAUUAUUUGAAUUAAUCGAU Drop Reaction, 5 day time UAAUUCAAAUAAUCAAUUAAUUAUUGG (SEQ ID  point NO: 248) Unseeded, Aggregated 61 GGAAAAUUUCAAAGUACUAUCAACUUUGAAUCAAG Drop Reaction, 5 day time UUCAAAGUUGAUAGUACUUUGAAUUUUGG point (SEQ ID NO: 249) Unseeded, Aggregated 62 GGAUGAUCAAUGUGUCCUGCAAUUCACAUUGAUU Drop Reaction, 5 day time CGAUCAAUGUGAAUUGCAGGACACAUUGAUCUUG point GGG (SEQ ID NO: 250) Unseeded, Aggregated 63 GGAAUAUUUAUCAAGCAUUCGAAAAUAUAUCCAAU Drop Reaction, 5 day time AUUUUCGAAUGCUUGAUAAAUAUUGG point (SEQ ID NO: 251) Unseeded, Aggregated 64 GGAAAGAAAUAUUUCUAAUUAACUACCUAGAUUUG Drop Reaction, 5 day time AAAUAUUUCUAAUAUUUCUAAUCUAGGUAGUUAAU point UAGAAAUAUUUCUUUGGG (SEQ ID NO: 252) Unseeded, Aggregated 65 GGUUUAAUUUAUCUGCAUCAAAUUCUGAUAAAUUA Drop Reaction, 5 day time AUUCCUUUAAUUUAUCAGAAUUUGAUGCAGAUAAA point UUAAAGGG (SEQ ID NO: 253) Unseeded, Aggregated 66 GGAUGAUCAAUGUGUCCUGCAAUUCACAUUCCGU Drop Reaction, 5 day time GAAUUCACAUUGAAUUCACGAUCAAUGUGAAUUG point CAGGACACAUUGAUCUUGG (SEQ ID NO: 254) Unseeded, Aggregated 67 GGAAAAUAUUUGAAUUGCAAUUCCCAAAUAUUUG Drop Reaction, 5 day time GGAAUUGCAAUUCAAAUAUUUGG (SEQ ID NO: 255) point Unseeded, Aggregated 68 GGAAAAAAUAAUAUGCAGGUGGGGCAUAUUAUUU Drop Reaction, 5 day time AAUUAAAAUAAUAUGCCCCACCUGCAUAUUAUUUU point UGGG (SEQ ID NO: 256) Unseeded, Aggregated 69 GGAUUUUAUCUCUCAACACCUCGAUGAUAAAUAU Drop Reaction, 5 day time CCCCAUUAUUUAUCAUCGAGGUGUUGAGAGAUAA point AUAAUGG (SEQ ID NO: 257) Unseeded, Aggregated 70 GGAAAUUUCAAAGAUUUAGUAACCACUUUGAAAAU Drop Reaction, 5 day time UUCAAAGUGGUUACUAAAUCUUUGAAAUUUGG point (SEQ ID NO: 258) Unseeded, Aggregated 71 GGAAAAUUCAAAGUCCAGUGCACUUUGAAUUUCA Drop Reaction, 5 day time AAAGAAAUUCAAAGUGCACUGGACUUUGAAUUCG point GG (SEQ ID NO: 259) Seeded with DNA pool, 1 GGAAUAUUUAUAUUCAAACUCGGAAUAUAAUAUAU Aggregated Drop Reaction, AUUUAUAUUCCGAGUUUGAAUAUAAAUAUUGG 5 day time point (SEQ ID NO: 260) Seeded with DNA pool, 2 GGAAAUUUGAUUUCUCAAAUUCAAAUUUAGAAUUC Aggregated Drop Reaction, CAAAUUUGAAUUUGAGAAAUCAAAUUUGG 5 day time point (SEQ ID NO: 261) Seeded with DNA pool, 3 GGAAUAUUUCUUAAUUUUCUCGUUGUUUAAGAAA Aggregated Drop Reaction, UAUUGAUUCCAAUAUUUUCUUAAACAACGAGAAAA 5 day time point UUAAGAAAUAUUGG (SEQ ID NO: 262) Seeded with DNA pool, 4 GGAAUGAUGAAUUCAUUCAACAUCAUUGAAUGAAU Aggregated Drop Reaction, GAUGAAUUCAUUCAAUUCAUUCAAUGAUGUUGAA 5 day time point UGAAUUCAUCAUUGGG (SEQ ID NO: 263) Seeded with DNA pool, 5 GGAAUAAUUUCAAUCUAAAUCUCCAGAUUGAAUAA Aggregated Drop Reaction, UUUCAAUCUGGAGAUUUAGAUUGAAAUUAUUGGG 5 day time point (SEQ ID NO: 264) Seeded with DNA pool, 6 GGAAUAAAAUUCAAUAUUUUCCUUAUAUAUUGAAU Aggregated Drop Reaction, AAAAUUCAAUAUAUAAGGAAAAUAUUGAAUUUUAU 5 day time point UGG (SEQ ID NO: 265) Seeded with DNA pool, 7 GGAAAAUUAAUCAAAUCUACCUGAUUUUGAUUUGA Aggregated Drop Reaction, AAUUAAUCAAAUCAAAAUCAGGUAGAUUUGAUUAA 5 day time point UUUUGG (SEQ ID NO: 266) Seeded with DNA pool, 8 GGAAAUAAAGAAUUUCGAUUCCUAUAUUCUUAUUU Aggregated Drop Reaction, GGAAUUUCCAAAUAAAGAAUAUAGGAAUCGAAAUU 5 day time point CUUUAUUUGGG (SEQ ID NO: 267) Seeded with DNA pool, 9 GGAAAAUUUCAAUUCAAAUUUGCCGAAAUUGAAAU Aggregated Drop Reaction, UUCAAUUCAAUUCGGCAAAUUUGAAUUGAAAUUUU 5 day time point GGG (SEQ ID NO: 268) Seeded with DNA pool, 10 GGAAAAAUAUUCUUCAAACUCAAUAUUGAAUAUUU Aggregated Drop Reaction, UUCCAAAAAUAUUCAAUAUUGAGUUUGAAGAAUAU 5 day time point UUUUGG (SEQ ID NO: 269) Seeded with DNA pool, 11 GGAAUAAAUAUCUGUUCAAUUAGUUCCCUAAUUU Aggregated Drop Reaction, GUUCAAUUAGGGAACUAAUUGAACAGAUAUUUAU 5 day time point UGG (SEQ ID NO: 270) Seeded with DNA pool, 12 GGAAAAUUCAAAGUCAACAAUUUGAAUUUCUCCAA Aggregated Drop Reaction, AAAUUCAAAUUGUUGACUUUGAAUUUUGGGG 5 day time point (SEQ ID NO: 271) Seeded with DNA pool, 13 GGAAAAUUUAUCUUAUCUACCCAACCUGAGAUAAA Aggregated Drop Reaction, UUUUGGAAUUUCAAAUUUAUCUCAGGUUGGGUAG 5 day time point AUAAGAUAAAUUUGG (SEQ ID NO: 272) Seeded with DNA pool, 14 GGGAAAAAUUGUUUCAAAUGCAGCAAACAAUUUU Aggregated Drop Reaction, GGCCAAAAUUGUUUGCUGCAUUUGAAACAAUUUU 5 day time point GG (SEQ ID NO: 273) Seeded with DNA pool, 15 GGAAAAACUAUUCAUUUGUCUCUAAUCAGAAUAGA Aggregated Drop Reaction, UUUUCCAAAAAACUAUUCUGAUUAGAGACAAAUGA 5 day time point AUAGUUUUUGG (SEQ ID NO: 274) Seeded with DNA pool, 16 GGAAAAUUAUCAAAAGUCGAUGAUAAUUUUGACCA Aggregated Drop Reaction, AAUUAUCAUCGACUUUUUGAUAAUUUUGG 5 day time point (SEQ ID NO: 275) Seeded with DNA pool, 17 GGAAAAUUCAAAAUAUUUGGUGAUAUUUUGAAUU Aggregated Drop Reaction, CAAAAUAUCACCAAAUAUUUUGAAUUUGGG 5 day time point (SEQ ID NO: 276) Seeded with DNA pool, 18 GGAAAUACUAUUUCAUCAUUCUCCUGAUGAUGAU Aggregated Drop Reaction, GAAAGAUGAAUACUAUUUCAUCUUUCAUCAUCAUC 5 day time point AGGAGAAUGAUGAAAUAGUAUUGG (SEQ ID NO: 277) Seeded with DNA pool, 19 GGGAAAAUUAUCAUUUGAAAGUGGUCAAAUGAAAA Aggregated Drop Reaction, UUAUCAUUUGACCACUUUCAAAUGAUAAUUUUGG 5 day time point (SEQ ID NO: 278) Seeded with DNA pool, 20 GGAAAAUUAAACUUUCACAAUCCUCCGUGAAAGU Aggregated Drop Reaction, GAUUAAACUUUCACGGAGGAUUGUGAAAGUUUAA 5 day time point UUUUGG (SEQ ID NO: 279) Seeded with DNA pool, 21 GGAAAUAAAACUUUUCAUAUUCAUAUUGAUGAAGU Aggregated Drop Reaction, UUUAUCCAAUAAAACUUCAUCAAUAUGAAUAUGAA 5 day time point AAGUUUUAUUUGG (SEQ ID NO: 280) Seeded with DNA pool, 22 GGAAAAAUUCAUCAAUGGAGAAUGUAUGAAUUUU Aggregated Drop Reaction, GUCCUAAAAUUCAUACAUUCUCCAUUGAUGAAUUU 5 day time point UGG (SEQ ID NO: 281) Seeded with DNA pool, 23 GGGGAAAAUUGAUCAUAGUAGUUCAUCAAUUUUU Aggregated Drop Reaction, CUUGCAAAAUUGAUGAACUACUAUGAUCAAUUUU 5 day time point GG (SEQ ID NO: 282) Seeded with DNA pool, 24 GGAAAAUUUGAUGGACUUAUGCAUACUUCAAAUU Aggregated Drop Reaction, UUCCCGAAAAUUUGAAGUAUGCAUAAGUCCAUCAA 5 day time point AUUUUGGG (SEQ ID NO: 283) Seeded with DNA pool, 25 GGAAAAUUAAUUUGGUACCAUACUUCACCCAAAUU Aggregated Drop Reaction, AAUUUUUGAAAUUUGAAUUUGGUGAAGUAUGGUA 5 day time point CCAAAUUAAUUUUGG (SEQ ID NO: 284) Seeded with DNA pool, 26 GGAAUUAGUUCAAUGUAUUUUUGACAAUGAAUUA Aggregated Drop Reaction, GUUCAAUGUCAAAAAUACAUUGAACUAAUUGG 5 day time point (SEQ ID NO: 285) Seeded with DNA pool, 27 GGAAAAUUUCAUAUUGUUAAUUACACAAUAUGAAC Aggregated Drop Reaction, AAUAUGAAAUUUCAUAUUGUUCAUAUUGUGUAAUU 5 day time point AACAAUAUGAAAUUUCGG (SEQ ID NO: 286) Seeded with DNA pool, 28 GGAAAGUUAAAUAAAUAAAUUCAAAUUCAAAUUCU Aggregated Drop Reaction, AUUUAUCUUUUCCAAAGUUAAAUAGAAUUUGAAUU 5 day time point UGAAUUUAUUUAUUUAACUUUGG (SEQ ID NO: 287) Seeded with DNA pool, 29 GGAAAUAUUUCCUAUUUGGGUAGUUAGGAAAUAU Aggregated Drop Reaction, UUUACCCAAAUAUUUCCCUAACUACCCAAAUAGGA 5 day time point AAUAUUUGGG (SEQ ID NO: 288) Seeded with DNA pool, 30 GGAAAAAUUAGAUUCUGCUAUCAAUCUAAUUUUCC Aggregated Drop Reaction, UAAAUUAGAUUGAUAGCAGAAUCUAAUUUUAGG 5 day time point (SEQ ID NO: 289) Seeded with DNA pool, 31 GGAAUAUCAAAAUCUAAUUAGGAGGCUAGAUUUG Aggregated Drop Reaction, AAAUAUCAAAUCUAGCCUCCUAAUUAGAUUUGAUA 5 day time point UUGG (SEQ ID NO: 290) Seeded with DNA pool, 32 GGAAAUUCAAUCUGAUGACUUUGAAUUUCAAUCU Aggregated Drop Reaction, GAAAAAUUCAAAGUCAUCAGAUUGAAUUUGG 5 day time point (SEQ ID NO: 291) Seeded with DNA pool, 33 GGAAUAUUCAAAUGCGUUGGAUUUGAAUAUUCAA Aggregated Drop Reaction, UGCAAUAUUCAAAUCCAACGCAUUGAAUAUUGG 5 day time point (SEQ ID NO: 292) Seeded with DNA pool, 34 GGAAAUUUGAAAGAAGAUUUGCUAAAAUUCAAAUU Aggregated Drop Reaction, UCCAAAUUGAAAUUUGAAUUUUUAGCAAAUCUUCU 5 day time point UUCAAAUUGG (SEQ ID NO: 293) Seeded with DNA pool, 35 GGAUAUUUUCAAUUUGUAUAGCAAGUCAAUACAAA Aggregated Drop Reaction, ACAAAAUUGACAUAUUUUCAAUUUGUUUUUGUAUU 5 day time point GACUUGCUAUACAAAUUGAAAAUAUGGG (SEQ ID NO: 294) Seeded with DNA pool, 36 GGAUGAUGAAUACUUCUAACAUUGUGAUCCCAGU Aggregated Drop Reaction, AUUCAUCGGAUGAAUACUGGGAUCACAAUGUUAG 5 day time point AAGUAUUCAUCUUGGG (SEQ ID NO: 295) Seeded with DNA pool, 37 GGGAAAACAAAUUGAAAAUUGUGGCAUUCACAAUU Aggregated Drop Reaction, UGUUUCCCAAAAACAAAUUGUGAAUGCCACAAUUU 5 day time point UCAAUUUGUUUUGGG (SEQ ID NO: 296) Seeded with DNA pool, 38 GGAAAAUAUUCAAAUUUUGAAUGAAUUCAAAUUUU Aggregated Drop Reaction, GAAUUCAUUCAAAAUUUGAAUAUUUUGGGG 5 day time point (SEQ ID NO: 297) Seeded with DNA pool, 39 GGAAUAAAAUGUGUUUAUUUGGUUAUUUUUCACA Aggregated Drop Reaction, UUUUUAUUCCCUAAAAAUGUGAAAAAUAACCAAAU 5 day time point AAACACAUUUUAGGG (SEQ ID NO: 298) Seeded with DNA pool, 40 GGAAAAAUUCAUAUUAUAGAAAUGAAUAAUAUGAA Aggregated Drop Reaction, AAAUUCAUAUUAUUCAUUUCUAUAAUAUGAAUUUU 5 day time point GG (SEQ ID NO: 299) Seeded with DNA pool, 41 GGAAGAAUCAAAUGAAUACUGUGAUGAACAGUGU Aggregated Drop Reaction, UUUAGUUCUUCCGAAGAACUAAAAAACACUGUUCA 5 day time point UCACAGUAUUCAUUUGAUUCUUGGG (SEQ ID NO: 300) Seeded with DNA pool, 42 GGAAUAUUCUUCAAUCUUCUACCUAGAUUGAUUG Aggregated Drop Reaction, GAUUGAUUGCAAUAUUCUUCAAUCCAAUCAAUCUA 5 day time point GGUAGAAGAUUGAAGAAUAUUGG (SEQ ID NO: 301) Seeded with DNA pool, 43 GGAAAUAUUUCAUAUUAUGUAUGGAAUCAUAAUUU Aggregated Drop Reaction, UAAUAUGAUGAAUAUUUCAUAUUAAAAAAAAUUAU 5 day time point GAUUCCAUACAUAAUAUGAAAUAUUUGG (SEQ ID NO: 302) Seeded with DNA pool, 44 GGAAAUUGCAAAUAUACAAUUCUAUAUCAUUCGAU Aggregated Drop Reaction, AUAGAAUUGUAUAUUGAAUUUUUUGG 5 day time point (SEQ ID NO: 303) Seeded with DNA pool, 45 GGAAAAAUCAAUAAUAUCUUUCCAAUCUGGAAAGA Aggregated Drop Reaction, UAUUAUUGGGAUAUUAUUUCCAAUAAUAUCUUUC 5 day time point CAGAUUGGAAAGAUAUUAUUGAUUUUUGG (SEQ ID NO: 304) Seeded with DNase-treated 1 GGAAAUUUUCAAUAAUUAAUUCCCAAAUUAUUGAA DNA pool, Aggregated Drop AUUUUCAAUAAUUUGGGAAUUAAUUAUUGAAAAUU Reaction, 5 day time point UGG (SEQ ID NO: 305) Seeded with DNase-treated 2 GGAAUAAUAUGAAAUGGAAUGGAUUCCUAUUAUU DNA pool, Aggregated Drop CCGAAUAAUAUGAAUCCAUUCCAUUUCAUAUUAUU Reaction, 5 day time point GG (SEQ ID NO: 306) Seeded with DNase-treated 3 GGAAUAAAUCAUUAAAUAUCAUUAUCGAUGAUUUA DNA pool, Aggregated Drop UCCAUAAAUCAUCGAUAAUGAUAUUUAAUGAUUUA Reaction, 5 day time point UGG (SEQ ID NO: 307) Seeded with DNase-treated 4 GGAAUAUUCAUUCAAUAUUCAUCUAUUGAAUAUAU DNA pool, Aggregated Drop UCAUUCAAUAUUCAAUAGAUGAAUAUUGAAUGAAU Reaction, 5 day time point AUUGG (SEQ ID NO: 308) Seeded with DNase-treated 5 GGAAAUUAUAUUGAGCUUCCAAUCCUCAAUAUAAU DNA pool, Aggregated Drop UUUAUAUUGAGGAUUGGAAGCUCAAUAUAAUUUG Reaction, 5 day time point G (SEQ ID NO: 309) Seeded with DNase-treated 6 GGAAAUUAUUUCUAUGUACCAUUUUGAAAUAAUUU DNA pool, Aggregated Drop CCCAAAUUAUUUCAAAAUGGUACAUAGAAAUAAUU Reaction, 5 day time point UGG (SEQ ID NO: 310) Seeded with DNase-treated 7 GGAAUAUUAUCACAAUAAUUUCCAUUUUGUGAAUA DNA pool, Aggregated Drop UUAUCACAAAAUGGAAAUUAUUGUGAUAAUAUUGG Reaction, 5 day time point (SEQ ID NO: 311) Seeded with DNase-treated 8 GGAAAUAAUUAAUUAAGAAGAUUAAUUAUUACCUA DNA pool, Aggregated Drop AUAAUUAAUCUUCUUAAUUAAUUAUUUGG Reaction, 5 day time point (SEQ ID NO: 312) Seeded with DNase-treated 9 GGAAAUAUUCAAAUGAGAAAAUAUCAUUUGAAAUA DNA pool, Aggregated Drop UUCAAAUGAUAUUUUCUCAUUUGAAUAUUUGG Reaction, 5 day time point (SEQ ID NO: 313) Seeded with DNase-treated 10 GGAAAUUAAUCAAAUUAAUUAAUUGAUUUGAUUUC DNA pool, Aggregated Drop AAAUUAAUCAAAUCAAUUAAUUAAUUUGAUUAAUU Reaction, 5 day time point GG (SEQ ID NO: 314) Seeded with DNase-treated 11 GGAAAAUUUCAUGUUGAAUUCCAAUCCCAACAACA DNA pool, Aggregated Drop UGAAAAUUUCAUGUUGGGAUUGGAAUUCAACAUG Reaction, 5 day time point AAAUUUGG (SEQ ID NO: 315) Seeded with DNase-treated 12 GGGAAAAUUCAAUUGAAAUCAAUUGGAAUCAAUUA DNA pool, Aggregated Drop AAAUUCAAUUGAUUCCAAUUGAUUUCAAUUGAAUU Reaction, 5 day time point UUGG (SEQ ID NO: 316) Seeded with DNase-treated 13 GGAAUGAAUCAAAUAAUUCAUUCAAUGAAUCAAAU DNA pool, Aggregated Drop AAUUCGAUGAAUUAUUUGAUUCAUUAUUGAAUGAA Reaction, 5 day time point UUAUUUUGAAUGG (SEQ ID NO: 317) Seeded with DNase-treated 14 GGAAAAAUAGAAUUCAAGUUAAACUAUUUUCUAUU DNA pool, Aggregated Drop UUUCCAAAAUAGAAAAUAGUUUAACUUGAAUUCUA Reaction, 5 day time point UUUUGG (SEQ ID NO: 318) Seeded with DNase-treated 15 GGAAAAUUAUAAUUGGAUUUGGAUAGACAAUUAUA DNA pool, Aggregated Drop AUUUGCAAAAUUAUAAUUGUCUAUCCAAAUCCAAU Reaction, 5 day time point UAUAAUUUGGG (SEQ ID NO: 319) Seeded with DNase-treated 16 GGAAAAUUAUCUAUACAUCUCCGAUAAUUUUCUUU DNA pool, Aggregated Drop CCAAAUUAUCGGAGAUGUAUAGAUAAUUUGGG Reaction, 5 day time point (SEQ ID NO: 320) Seeded with DNase-treated 17 GGAAAUUGAAUCAAUUAGAUGAUUUAAUUGAAAUU DNA pool, Aggregated Drop GAAUCAAUUAAAUCAUCUAAUUGAUUCAAUUUGG Reaction, 5 day time point (SEQ ID NO: 321) Seeded with DNase-treated 18 GGGAAUUUCAUAAGUUCAUCGUUUGCUUAUGAAA DNA pool, Aggregated Drop CAAUUUCAUAAGCAAACGAUGAACUUAUGAAAUUG Reaction, 5 day time point G (SEQ ID NO: 322) Seeded with DNase-treated 19 GGGAAGAUAUAUCAAAGAAAUAUAUUUUUCCCAAA DNA pool, Aggregated Drop AAUAUAUUUCUUUGAUAUAUCUUGG Reaction, 5 day time point (SEQ ID NO: 323) Seeded with DNase-treated 20 GGAAAAUUUAUCUUUGGUAAAUUUGAUAAAUUUUA DNA pool, Aggregated Drop AUCCAAAUUUAUCAAAUUUACCAAAGAUAAAUUUG Reaction, 5 day time point G (SEQ ID NO: 324) Seeded with DNase-treated 21 GGAAAUUUCAAUUUCAAUUGGAAUUAAUUGAAAUU DNA pool, Aggregated Drop UCAAUUUCAAUUAAUUCCAAUUGAAAUUGAAAUUU Reaction, 5 day time point GG (SEQ ID NO: 325) Seeded with DNase-treated 22 GGAAAAUUUGUUAUGUAUGCAUUGGACAAAUUUU DNA pool, Aggregated Drop CCCAAUUUGUCCAAUGCAUACAUAACAAAUUGGG Reaction, 5 day time point (SEQ ID NO: 326) Seeded with DNase-treated 23 GGAAAUUCAAUUUCAAUUACAAUUGAGUUGUAAUU DNA pool, Aggregated Drop GAAUUUGGUUAUCCAAAUUCAAUUACAACUCAAUU Reaction, 5 day time point GUAAUUGAAAUUGAAUUUGG (SEQ ID NO: 327) Seeded with DNase-treated 24 GGAAUAAUAUCUAUUUAUUAUUAUUGAUAGAUAUU DNA pool, Aggregated Drop AUUUAAUAAUAUCUAUCAAUAAUAAUAAAUAGAUA Reaction, 5 day time point UUAUUGG (SEQ ID NO: 328) Seeded with DNase-treated 25 GGAAUUAAUUUCAAUUCUAUUCAGUAAUUGAUUAA DNA pool, Aggregated Drop UUUCAAUUACUGAAUAGAAUUGAAAUUAAUGG Reaction, 5 day time point (SEQ ID NO: 329) Seeded with DNase-treated 26 GGAAAUUUAUCAUAUUCAUGGGGUAGAUCAUAUA DNA pool, Aggregated Drop UGAUGAAUUUAUCAUAUAUGAUCUACCCCAUGAAU Reaction, 5 day time point AUGAUAAAUUUGG (SEQ ID NO: 330) Seeded with DNase-treated 27 GGAUUUAAUCUUUGCCUCUAAAAAGAUUAAUCCAU DNA pool, Aggregated Drop UUAAUCUUUUUUAGAGGCAAAGAUUAAAUGG Reaction, 5 day time point (SEQ ID NO: 331) Seeded with DNase-treated 28 GGGAUAUUAUCAUAUAUGUUUGAUGACAUAUAUC DNA pool, Aggregated Drop AUAUAUGUCAUCAAACAUAUAUGAUAAUAAGG Reaction, 5 day time point (SEQ ID NO: 332) Seeded with DNase-treated 29 GGAAAAUUAUUUUCAAAUAAAGGUCUCUAUUAAUU DNA pool, Aggregated Drop AUUUUCAAAUAAUAGAGACCUUUAUUUGAAAAUAA Reaction, 5 day time point UUUUGG (SEQ ID NO: 333) Seeded with DNase-treated 30 GGAAAAUUUCAAAUUGAAAAUCAAAUUUGAAAAUU DNA pool, Aggregated Drop UCAAAUUUGAUUUUCAAUUUGAAAUUUUGG Reaction, 5 day time point (SEQ ID NO: 334) Seeded with DNase-treated 31 GGAAAAAUUAUCAUGUACUCUAAUCCAUGAUAAAA DNA pool, Aggregated Drop UUAUCAUGGAUUAGAGUACAUGAUAAUUUUGG Reaction, 5 day time point (SEQ ID NO: 335) Seeded with DNase-treated 32 GGAAAAAUUAGAAAGAAAACCUAAUUUUUCCAAAA DNA pool, Aggregated Drop AUUAGGUUUUCUUUCUAAUUUUUGG Reaction, 5 day time point (SEQ ID NO: 336) Seeded with DNase-treated 33 GGGAAAUUUGGAUUCUCUUCUCUUCCUAAUCCAA DNA pool, Aggregated Drop AUUUCCCAAAUUUGGAUUAGGAAGAGAAGAGAAU Reaction, 5 day time point CCAAAUUUGG (SEQ ID NO: 337) Seeded with DNase-treated 34 GGAAAUUUGAUUAAUUCAUUUGGAAAUUUGAUUA DNA pool, Aggregated Drop AUUUCCAAAUGAAUUAAUCAAAUUUGG Reaction, 5 day time point (SEQ ID NO: 338) Seeded with DNase-treated 35 GGGAAAUUUCUUUCAACAGAGAUAGUUUGUUGAA DNA pool, Aggregated Drop UUUCUUUCAACAAACUAUCUCUGUUGAAAGAAAUU Reaction, 5 day time point UGG (SEQ ID NO: 339) Seeded with DNase-treated 36 GGAAAUUUCAUCUUGAAUUGUAAUCCCGAGAUUA DNA pool, Aggregated Drop AAUUUCAUCUCGGGAUUACAAUUCAAGAUGAAAUU Reaction, 5 day time point UGGG (SEQ ID NO: 340) Seeded with DNase-treated 37 GGAAAUUAUCUUAAUUAUCUUAUCAAAUUAGAUAA DNA pool, Aggregated Drop GAUAAGAUAAUUAUCUAUCUUAUCUUAUCUAAUUU Reaction, 5 day time point GAUAAGAUAAUUAAGAUAAUUUGGG (SEQ ID NO: 341) Seeded with DNase-treated 38 GGAUAAUAAUGGAUUAUUGGUGAUGUUCCAUUAU DNA pool, Aggregated Drop UAUCCGAUAAUAAUGGAACAUCACCAAUAAUCCAU Reaction, 5 day time point UAUUAGG (SEQ ID NO: 342) Seeded with DNase-treated 39 GGAUUUGAAUCAAAUCAAAUCAAAUCAAAUCAUUU DNA pool, Aggregated Drop GAUUUGAUUUGAUUUGCUAAUCAAAUGG Reaction, 5 day time point (SEQ ID NO: 343) Seeded with DNase-treated 40 GGAAAUGAAAUAAUAUCCAUCAUUCUAUUAUUUUU DNA pool, Aggregated Drop UCCAAAUGAAAUAAUAGAAUGAUGGAUAUUAUUUC Reaction, 5 day time point AUUUGG (SEQ ID NO: 344) Seeded with DNase-treated 41 GGAAAAUUACAAAGUUCCAGUGUAAUUUUGUAAU DNA pool, Aggregated Drop UUCCAAUUACAAAAUUACACUGGAACUUUGUAAUU Reaction, 5 day time point UGG (SEQ ID NO: 345) Seeded with DNase-treated 42 GGAAAAUAAUGGAUCAAAUAACUGUAUCAUUCAUU DNA pool, Aggregated Drop AUUUUCCAAAAUAAUGAAUGAUACAGUUAUUUGAU Reaction, 5 day time point CCAUUAUUUUGG (SEQ ID NO: 346) Seeded with DNase-treated 43 GGAAUGAAUAUACAGGAUAAAUUAUUCACUUCAUG DNA pool, Aggregated Drop UAUAUUCAUUCCCAUGAAGUGAAUAAUUUAUCCU Reaction, 5 day time point GUAUAUUCAUGG (SEQ ID NO: 347) Seeded with DNase-treated 44 GGAAAUAAAUUAGUCUUUCCUAAAUAAUUAGACUA DNA pool, Aggregated Drop AAUUAAAUAAAUUAGUCUAAUUAUUUAGGAAAGAC Reaction, 5 day time point UAAUUUAUUUGG (SEQ ID NO: 348) Seeded with DNase-treated 45 GGAAAUAUAUAUUUGGUUUUUCAUCCCCAAAUAUA DNA pool, Aggregated Drop UAUUUAUAUUUGGGGAUGAAAACCAAAUAUAUAUU Reaction, 5 day time point UGGG (SEQ ID NO: 349) Seeded with DNase-treated 46 GGAAAAUUUAGGAGUGCUUGUAAGUUUCCAUCCU DNA pool, Aggregated Drop AAUUUUCCCAAUUUAGGAUGGAAACUUACAAGCAC Reaction, 5 day time point UCCUAAAUUUGG (SEQ ID NO: 350) Seeded with DNase-treated 47 GGAAAUAUUCAAAAGAUUUCAUCCUUUUGAAUAUU DNA pool, Aggregated Drop UUCUUUGAAAUAUUCAAAAGAAAAUAUUCAAAAGG Reaction, 5 day time point AUGAAAUCUUUUGAAUAUUUGG (SEQ ID NO: 351) Seeded with DNase-treated 48 GGAGAAAUAAAUUUGGUAUACUGCACAUUUCAAU DNA pool, Aggregated Drop UUAUUUCUCGAGAAAUAAAUUGAAAUGUGCAGUA Reaction, 5 day time point UACCAAAUUUAUUUCUGGG (SEQ ID NO: 352) Seeded with DNase-treated 49 GGAAAAUUUGAUUCAAAUACUUCAUAUUUGAUUCA DNA pool, Aggregated Drop AAUAUGAAGUAUUUGAAUCAAAUUUUGG Reaction, 5 day time point (SEQ ID NO: 353) Seeded with DNase-treated 50 GGGAAAAUUCAUUUCAUUUGCAAAUGAAUUCAUU DNA pool, Aggregated Drop UCAAUUCAUUUGCAAAUGAAAUGAAUUUGG Reaction, 5 day time point (SEQ ID NO: 354) Seeded with DNase-treated 51 GGAAAUCAAAUUAUCUUCAUCCCCAUUUCAGAUAA DNA pool, Aggregated Drop UUUGAGAAUCAAAUUAUCUGAAAUGGGGAUGAAG Reaction, 5 day time point AUAAUUUGAUUUGG (SEQ ID NO: 355) Seeded with DNase-treated 52 GGAAUAUUGGUUUUGGUAUUUGCACUUUCCAAUA DNA pool, Aggregated Drop UUCCCCAAUAUUGGAAAGUGCAAAUACCAAAACCA Reaction, 5 day time point AUAUUGG (SEQ ID NO: 356) Seeded with DNase-treated 53 GGAAAUUGCAAUGUUAGAUUCUUUCCUCAAAUUG DNA pool, Aggregated Drop CAAUUUCAGUUUUUUCCAAUUUGAGGAAAGAAUC Reaction, 5 day time point UAACAUUGCAAUUUGG (SEQ ID NO: 357) Seeded with DNase-treated 54 GGGAAAUUAUUCAUAGUUCUGCCUAUGAAAAUUA DNA pool, Aggregated Drop UUCAUAGGCAGAACUAUGAAUAAUUUAGG Reaction, 5 day time point (SEQ ID NO: 358) Seeded with DNase-treated 55 GGAUAUUCAAAUCAUUAGCAAAUCCUAAUGAUGAU DNA pool, Aggregated Drop UUGAAAUCCAUAUUCAAAUCAUCAUUAGGAUU UGC Reaction, 5 day time point UAAUGAUUUGAAUAUGG (SEQ ID NO: 359) Seeded with DNase-treated 56 GGAAAUUUUGGAAAUUGAAUGGAAUCCAAAAUUU DNA pool, Aggregated Drop UCCGAAAUUUUGGAUUCCAUUCAAUUUCCAAAAUU Reaction, 5 day time point UGGG (SEQ ID NO: 360) Seeded with DNase-treated 57 GGGAAAAUGGAAUUGAAUGGAAAUUUCCAUUUUC DNA pool, Aggregated Drop CAAAUGGAAAAUGAUGAAAUUUCCAUUCAAUUCCA Reaction, 5 day time point UUUGG (SEQ ID NO: 361) Seeded with DNase-treated 58 GGAAAAUUCAAAUAAUUAGAGAUUGCAUAUUAUUU DNA pool, Aggregated Drop GAAUUGAUUGCAUAUAAAUUCAAAUAAUAUGCAAU Reaction, 5 day time point CUCUAAUUAUUUGAAUUUUGG (SEQ ID NO: 362) Seeded with DNase-treated 59 GGAAAAUUCAAAAUUCGAAUUUGAAUUUGGAAAAU DNA pool, Aggregated Drop UUCCAAAUUCAAAUUCGAAUUUUGAAUUUGG Reaction, 5 day time point (SEQ ID NO: 363) Seeded with DNase-treated 60 GGAAAUUUCAAAUUUCAAUCAUCGAAAUUUCAAAU DNA pool, Aggregated Drop UUCGAUGAUUGAAAUUUGAAAUUUGGGG Reaction, 5 day time point (SEQ ID NO: 364) Seeded with DNase-treated 61 GGAUAAAUUCAUUAUCUUCAAUUCUCCAGAUAAUG DNA pool, Aggregated Drop AAUUUUGAUUAUCAAAAAUUCAUUAUCUGGAGAAU Reaction, 5 day time point UGAAGAUAAUGAAUUUCGG (SEQ ID NO: 365) Seeded with DNase-treated 62 GGAAAUAUUCAAUAUUUCACAGGUCACUGUGAAA DNA pool, Aggregated Drop UAUUUGGAAUAUUGUCCAAAUUCCAAAUAUUUCAC Reaction, 5 day time point AGUGACCUGUGAAAUAUUGAAUAUUUGGG (SEQ ID NO: 366) Seeded with DNase-treated 63 GGAAAAUUGAAUACUUCAUUGCAUUCCAUUCAAUU DNA pool, Aggregated Drop UUCCCAAAAUUGAAUGGAAUGCAAUGAAGUAUUCA Reaction, 5 day time point AUUUUGGG (SEQ ID NO: 367) Seeded with DNase-treated 64 GGAAAUUAAUCAAUAAAUUUAGUGCAAUUCAUUAA DNA pool, Aggregated Drop UCAAUAAAUAAUGAAUUGCACUAAAUUUAUUGAUU Reaction, 5 day time point AAUUUGG (SEQ ID NO: 368) Seeded with DNase-treated 65 GGAAAUUUGGUCUCUUGUCACAUCAUCCAAAUUU DNA pool, Aggregated Drop CCCCCAAAUUUGGAUGAUGUGACAAGAGACCAAA Reaction, 5 day time point UUUGG (SEQ ID NO: 369) Seeded with DNase-treated 66 GGAAAUUUGAAAUUUCAAAAUCAAAUGAUUUUGAA DNA pool, Aggregated Drop AUUUCAAAAUCAUUUGAUUUUGAAAUUUCAAAUUC Reaction, 5 day time point GG (SEQ ID NO: 370) Seeded with DNase-treated 67 GGAAAUAUUUUCUUUUCUAGCAUAUCUAGAAAUAU DNA pool, Aggregated Drop UGAAAAAUAUUUUCUUUUUUCCCAAUAUUUCUAGA Reaction, 5 day time point UAUGCUAGAAAAGAAAAUAUUGG (SEQ ID NO: 371) Seeded with DNase-treated 68 GGAAUAUUGAAUUAAUGUAAUCCACCCACAUUAAU DNA pool, Aggregated Drop UCACAUUGAAUUAAUGUGGUGGAUUACAUUAAUU Reaction, 5 day time point CAAUAUUGG (SEQ ID NO: 372) Seeded with DNase-treated 69 GGAAAUUUAAAUACAAUUCCAAGUGCCUUGAAUU DNA pool, Aggregated Drop GUAUUUAAAUACAAUUCAAGGCACUUGGAAUUGU Reaction, 5 day time point AUUUAAAUUUGG (SEQ ID NO: 373) Seeded with DNase-treated 70 GGAAAUUUCUCAAAAUUUGACUUGAAAUUUCUCAA DNA pool, Aggregated Drop AAUUCAAGUCAAAUUUUGAGAAAUUUGG Reaction, 5 day time point (SEQ ID NO: 374) Seeded with DNase-treated 71 GGAAAAUAUUCUUCAACAUUAUAUUUGGUUCAUUA DNA pool, Aggregated Drop CAAGUUGAAAUAAUAUUCUUCAACAUUAUUUCAAC Reaction, 5 day time point UUGUAAUGAACCAAAUAUAAUGUUGAAGAAUAUUU UGGG (SEQ ID NO: 375) Seeded with DNase-treated 72 GGAAUUAUUGGAAUUUGGCUAUCUUAUUAAUCCA DNA pool, Aggregated Drop AUAAUUUGGCAAUUAUUGGAUUAAUAAGAUAGCCA Reaction, 5 day time point AAUUCCAAUAAUUGGG (SEQ ID NO: 376) Seeded with DNase-treated 73 GGAAAUAUCAAUCAAAGCCUUAUAUUUGAUUUUUC DNA pool, Aggregated Drop CAAAUAUCAAAUAUAAGGCUUUGAUUGAUAUUUG Reaction, 5 day time point G (SEQ ID NO: 377) Seeded with DNase-treated 74 GGAAUAUUUGCUUUCUUUGAUUAUAUUCUUUGCA DNA pool, Aggregated Drop AAUAUUCCCAAAUAUUUGCAAAGAAUAUAAUCAAA Reaction, 5 day time point GAAAGCAAAUAUUGGG (SEQ ID NO: 378) Seeded with DNase-treated 75 GGAAAUAAACUUCCAUAUAAUAUUGGAAUAUAUUA DNA pool, Aggregated Drop UAUAUGGAAUAAACUUCCAUAUAUAAUAUAU UCCA Reaction, 5 day time point AUAUUAUAUGGAAGUUUAUUGGG (SEQ ID NO: 379) Seeded with DNase-treated 76 GGAAAAAUUGGAUAUUGCUGACUCGUUCCCAAUU DNA pool, Aggregated Drop UUUCCCGGAAAAUUGGAACGAGUCAGCAAUAUCC Reaction, 5 day time point AAUUUUGG (SEQ ID NO: 380) Seeded with DNase-treated 77 GGGAAAUUUGAAUCUCUGCUCCAUUCAAAUUUCC DNA pool, Aggregated Drop AAAUUUGAAUGGAGCAGAGAUUCAAAUUUGGG Reaction, 5 day time point (SEQ ID NO: 381) Seeded with DNase-treated 78 GGAAAUAAUCAAUAGUUUUACCAACCCUACUAUUG DNA pool, Aggregated Drop AUUAAUAAUCAAUAGUAGGGUUGGUAAACUAUUG Reaction, 5 day time point AUUAUUGG (SEQ ID NO: 382) Seeded with DNase-treated 79 GGAAAAUUAGGAAUUUUGUAGCAUUUCCAUUUCC DNA pool, Aggregated Drop UAAUUUUCUACAAAAUUAGGAAAUGGAAAUGCUAC Reaction, 5 day time point AAAAUUCCUAAUUUUGGG (SEQ ID NO: 383) Seeded with DNase-treated 80 GGAAAUAAAGAAGUAUUUCUCUUUUCCUUAUUUC DNA pool, Aggregated Drop UCUUUUCUAAAUAAAGAAAUAAGGAAAAGAGAAAU Reaction, 5 day time point ACUUCUUUAUUUGG (SEQ ID NO: 384) Seeded with DNase-treated 81 GGAAUAAUUCUAUUCGAUUCCUAGAAUUUUCAUU DNA pool, Aggregated Drop CCAUAAUUCUAGGAAUCGAAUAGAAUUAUGG Reaction, 5 day time point (SEQ ID NO: 385) Seeded with DNase-treated 82 GGAUUGAUUAAAUCAAUAAGGAAUGGCUUCUUCA DNA pool, Aggregated Drop UUUAUUGAAGAAGCCAUUCCUUCCUUAUUGAUUU Reaction, 5 day time point CAAGG (SEQ ID NO: 386) Seeded with DNase-treated 83 GGAAAAGAACUAUUUCAAUUCCAUUCUUUUGGAA DNA pool, Aggregated Drop UGAAAUAGAUUCUUUCUAUUUCAUUCCAAAAGAAU Reaction, 5 day time point GGAAUUGAAAUAGUUCUUUUGG (SEQ ID NO: 387) Seeded with DNase-treated 84 GGAAAAUUGGAAAUCAUCAUUCUCAUCCAAUUUUC DNA pool, Aggregated Drop CAAAAUUGGAUGAGAAUGAUGAUUUCCAAUUUUG Reaction, 5 day time point GG (SEQ ID NO: 388) Seeded with hot alkali- 1 GGAAUAAAUUGGACUACUUAAUACACAAUUUAUUC treated DNA pool, CAAUAAAUUGUGUAUUAAGUAGUCCAAUUUAUUG Aggregated Drop Reaction, G (SEQ ID NO: 389) 5 day time point Seeded with hot alkali- 2 GGAAAUAACAUUUUCAUCUCACAUCAGAAAUGUUA treated DNA pool, AUUCCAAAUAACAUUUCUGAUGUGAGAUGAAAAUG Aggregated Drop Reaction, UUAUUUGGG (SEQ ID NO: 390) 5 day time point Seeded with hot alkali- 3 GGAAUAAUUCAAUAAUUCCUAUAUUAUUGAAAUAA treated DNA pool, UUCAAUAAUAUAGGAAUUAUUGAAUUAUUGG Aggregated Drop Reaction, (SEQ ID NO: 391) 5 day time point Seeded with hot alkali- 4 GGAAUAUUUCAGAAUUCAAUUACAUCAAUUCCGAA treated DNA pool, UAUUUUCCAAUAUUCGGAAUUGAUGUAAUUGAAU Aggregated Drop Reaction, UCUGAAAUAUUGG (SEQ ID NO: 392) 5 day time point Seeded with hot alkali- 5 GGAAAUUUCAAUGUUAUCAUUACACAUUGAAAAUU treated DNA pool, UCAAUGUGUAAUGAUAACAUUGAAAUUUGG Aggregated Drop Reaction, (SEQ ID NO: 393) 5 day time point Seeded with hot alkali- 6 GGAUAUUACAUUAUCAAUCCUUGCGAUGUAAUUG treated DNA pool, AUCCUAUUACAUCGCAAGGAUUGAUAAUGUAAUA Aggregated Drop Reaction, GG (SEQ ID NO: 394) 5 day time point Seeded with hot alkali- 7 GGAAAUUAUCAUUUCUGAUCAAAGAUAUGAUUCAA treated DNA pool, UUAUCAUAUCUUUGAUCAGAAAUGAUAAUUUGG Aggregated Drop Reaction, (SEQ ID NO: 395) 5 day time point Seeded with hot alkali- 8 GGAAAAUUUCAAAUUAUUGUGGCUGAAAUUUGAA treated DNA pool, AUUUCCAAAUUUCAAAUUUCAGCCACAAUAAUUUG Aggregated Drop Reaction, AAAUUUUGGG (SEQ ID NO: 396) 5 day time point Seeded with hot alkali- 9 GGAAAAUUUCAAAUAAUGCCGAUUAUUUGAAAAUU treated DNA pool, UCAAAUAAUCGGCAUUAUUUGAAAUUUUGG Aggregated Drop Reaction, (SEQ ID NO: 397) 5 day time point Seeded with hot alkali- 10 GGAAAUUUCAAACAAAUUUGUUGUGUGUUGUUUG treated DNA pool, AAUUUCAAACAAAUUUCAAAACAACACACAACAAAU Aggregated Drop Reaction, UUGUUUGAAAUUUGG (SEQ ID NO: 398) 5 day time point Seeded with hot alkali- 11 GGAAAUUUACCAAUUCAUGGGGUGGUGAAUUUAC treated DNA pool, CAAUUUACCACCCCAUGAAUUGGUAAAUUGGG Aggregated Drop Reaction, (SEQ ID NO: 399) 5 day time point Seeded with hot alkali- 12 GGGGAAUUUCAUUCAAUUACCCGAUUGAUGAAAU treated DNA pool, UUCAUUCAAUCGGGUAAUUGAAUGAAAUUGG Aggregated Drop Reaction, (SEQ ID NO: 400) 5 day time point Seeded with hot alkali- 13 GGAAUAAUUGAUAUAAUGCGUCAAUCAAUUCAAUU treated DNA pool, AUUCCAUAAUUGAAUUGAUUGACGCAUUAUAUCAA Aggregated Drop Reaction, UUAUGGG (SEQ ID NO: 401) 5 day time point Seeded with hot alkali- 14 GGAAUAUUUCAAGAAUGUUUAUCCUUAUCCAUUC treated DNA pool, UUUUGAAUAUUCAAGAAUGGAUAAGGAUAAACAUU Aggregated Drop Reaction, CUUGAAAUAUUGG (SEQ ID NO: 402) 5 day time point Seeded with hot alkali- 15 GGAAAAUUUCGAAAUUUCCGAAAUAUCGAAAUAUC treated DNA pool, CAAAUUUCGAUAUUUCGGAAAUUUCGAAAUUUUG Aggregated Drop Reaction, G (SEQ ID NO: 403) 5 day time point Seeded with hot alkali- 16 GGAAAAUUAUCAAUUGCACUCUUGCAAAUUGAAAU treated DNA pool, UAUCAAUUUGCAAGAGUGCAAUUGAUAAUUUUGG Aggregated Drop Reaction, G (SEQ ID NO: 404) 5 day time point Seeded with hot alkali- 17 GGAAAUGUUUAUGUUUCUUUGCGAUUUUCCAUAA treated DNA pool, ACAUUUUGCAAAUGUUUAUGGAAAAUCGCAAAGAA Aggregated Drop Reaction, ACAUAAACAUUUGG (SEQ ID NO: 405) 5 day time point Seeded with hot alkali- 18 GGAAAAUUCAAAUCAUUUAGAGUUCGGAUUUAAAU treated DNA pool, UUUCCAAAUUCAAAUCCGAACUCUAAAUGAUUUGA Aggregated Drop Reaction, AUUUUGG (SEQ ID NO: 406) 5 day time point Seeded with hot alkali- 19 GGAAAUUGAAAUGCAUUUCAAAUUCAAUUUUCCAA treated DNA pool, AUUGAAAAUUGAAUUGAAAUGCAUUUCAAUUUGG Aggregated Drop Reaction, G (SEQ ID NO: 407) 5 day time point Seeded with hot alkali- 20 GGAAAAUAAUCAAUUCCGGAUUAUUGAUUAUUAUU treated DNA pool, UCCAAUAAUCAAUAAUCCGGAAUUGAUUAUUUGG Aggregated Drop Reaction, (SEQ ID NO: 408) 5 day time point Seeded with hot alkali- 21 GGAAAAAUUGAUUCGAUCAUUUCAAUUUUUUCCG treated DNA pool, AAAAAUUGAAAUGAUCGAAUCAAUUUUUGG Aggregated Drop Reaction, (SEQ ID NO: 409) 5 day time point Seeded with hot alkali- 22 GGAAUAUUAAAUACUUUAUUCUCCCAAUAUUAAAU treated DNA pool, ACUUUAUUCGGAAUAAAGUAUUUAAUAUUGGGAG Aggregated Drop Reaction, AAUAAAGUAUUUAAUAUUGG (SEQ ID NO: 410) 5 day time point Seeded with hot alkali- 23 GGAAAAUAUUUGGCAUAUAAUAUGUAUAAUAUUUU treated DNA pool, CCCAAAUAUUAUACAUAUUAUAUGCCAAAUAUUUG Aggregated Drop Reaction, GG (SEQ ID NO: 411) 5 day time point Seeded with hot alkali- 24 GGAAAAUUAAUUAUCAAAAAGCUGUUCCUUUAAUU treated DNA pool, AUCAAAAAGGAACAGCUUUUUGAUAAUUAAUUUUG Aggregated Drop Reaction, G (SEQ ID NO: 412) 5 day time point Seeded with hot alkali- 25 GGAAAUUAUCAUUUCUGAUCAACCCGGAAAUGAA treated DNA pool, UUAUCAUUUCCGGGUUGAUCAGAAAUGAUAAUUU Aggregated Drop Reaction, GG (SEQ ID NO: 413) 5 day time point Seeded with hot alkali- 26 GGAAUUUUUCAAACUUUGGAUCCAGUUUGAAUUU treated DNA pool, UCAAACUGGAUCCAAAGUUUGAAAAUUGG Aggregated Drop Reaction, (SEQ ID NO: 414) 5 day time point Seeded with hot alkali- 27 GGAAAAUUUCAAUGAUCGAUGGGAGCAUUGAAAU treated DNA pool, UUCAAUGCUCCCAUCGAUCAUUGAAAUUUUGGG Aggregated Drop Reaction, (SEQ ID NO: 415) 5 day time point Seeded with hot alkali- 28 GGAAUAUUUGAAAAGUUUGGACUUCUUUUCAAAU treated DNA pool, AUUGAAAAGAAGUCCAAACUUUUCAAAUAUUGG Aggregated Drop Reaction, (SEQ ID NO: 416) 5 day time point Seeded with hot alkali- 29 GGAAAUAUUCAAAAUCUACCCUUGAAUAUUUUUCC treated DNA pool, AAAUAUUCAAGGGUAGAUUUUGAAUAUUUGG Aggregated Drop Reaction, (SEQ ID NO: 417) 5 day time point Seeded with hot alkali- 30 GGAAUAUAUCUGAUUGUCUAUUUAGAUAUUUUCC treated DNA pool, AAUAUAUCUAAAUAGACAAUCAGAUAUAUUGG Aggregated Drop Reaction, (SEQ ID NO: 418) 5 day time point Seeded with hot alkali- 31 GGAAAAUUGGAUAUUCGUAGUUGCUUCCAAUUUU treated DNA pool, CCCGAAAAAUUGGAAGCAACUACGAAUAUCCAAUU Aggregated Drop Reaction, UUGG (SEQ ID NO: 419) 5 day time point Seeded with hot alkali- 32 GGAACUUUUCAUAAAUCUCCUCAACAGUGCGAUG treated DNA pool, AACUUUUCAUAAAUCGCACUGUUGAGGAGAUUUA Aggregated Drop Reaction, UGAAAAGUUGG (SEQ ID NO: 420) 5 day time point Seeded with hot alkali- 33 GGAUUUUUAGUCAUUUUCAAAACGCGUCUGACUA treated DNA pool, AAAAAGCCAUUUUUAGUCAGACGCGUUUUGAAAA Aggregated Drop Reaction, UGACUAAAAAUGG (SEQ ID NO: 421) 5 day time point Seeded with hot alkali- 34 GGAAAAAUUCAACUUUUUGUGCGUUGAGUUGAAU treated DNA pool, UUUCCAAAAAUUCAACUCAACGCACAAAAAGUUGA Aggregated Drop Reaction, AUUUUGG (SEQ ID NO: 422) 5 day time point Seeded with hot alkali- 35 GGAAAAUUUCAUGAUCUUUUCUCUUGGGAAAUUU treated DNA pool, CAUAAUUUUUCCCAAGAGAAAAGAUCAUGAAAUUU Aggregated Drop Reaction, GG (SEQ ID NO: 423) 5 day time point Seeded with hot alkali- 36 GGAAUUAAUCAAACUCAUCUUUUCUAUUGUUUGA treated DNA pool, AUUAAUCAAACAAUAGAAAAGAUGAGUUUGAUUAA Aggregated Drop Reaction, UUGGG (SEQ ID NO: 424) 5 day time point Seeded with hot alkali- 37 GGAAAUUCUCUUUCAAUAUUCAAGAAUUUGAGAAU treated DNA pool, UUCUUUCCAAAUUCUCAAAUUCUUGAAUAUUGAAA Aggregated Drop Reaction, GAGAAUUUGGG (SEQ ID NO: 425) 5 day time point Seeded with hot alkali- 38 GGAAAAAUUCUAAUAAGUAUCAACUUUCUGAAUUA treated DNA pool, UUCCAAAAUUCAGAAAGUUGAUACUUAUUAGAAUU Aggregated Drop Reaction, UUGG (SEQ ID NO: 426) 5 day time point Seeded with hot alkali- 39 GGGAAAUCAAUUGGAAUAAGCCCAAAAUUGAUUU treated DNA pool, CAAAUCAAUUUGGGCUUAUUCCAAUUGAUUUGGG Aggregated Drop Reaction, G (SEQ ID NO: 427) 5 day time point Seeded with hot alkali- 40 GGGGGAAAUUUGUAUUUCAUCAAAUGAUGAUUUC treated DNA pool, AUCAAAUGAUGAAAUCAUCAUUUGAUGAAAUACAA Aggregated Drop Reaction, AUUUGG (SEQ ID NO: 428) 5 day time point Seeded with hot alkali- 41 GGAAAUUCAAUCUAUAACAGUCAUAUAGUUUGAAA treated DNA pool, AAUUCAAUCUAUAUGACUGUUAUAGAUUGAAUUU Aggregated Drop Reaction, GG (SEQ ID NO: 429) 5 day time point Seeded with hot alkali- 42 GGGAAAUAUUGUUGUGUAUUGGAUGUUGAGUUCG treated DNA pool, UAACAAUAUUCCGAAUAUUGUUACGAACUCAACAU Aggregated Drop Reaction, CCAAUACACAACAAUAUUUGG (SEQ ID NO: 430) 5 day time point Seeded with hot alkali- 43 GGAAAUUGGAAUAAAUGGUUUAUUACAAUUUCCAA treated DNA pool, AUUGGAAAUUGUAAUAAACCAUUUAUUCCAAUUUG Aggregated Drop Reaction, GG (SEQ ID NO: 431) 5 day time point Seeded with hot alkali- 44 GGAAAAUUGGAAAUUGAGCAACUGUACCAAUUUU treated DNA pool, CCCGAAAAUUGGUACAGUUGCUCAAUUUCCAAUU Aggregated Drop Reaction, UUGGG (SEQ ID NO: 432) 5 day time point Seeded with hot alkali- 45 GGAAUAAUUGAAUUACAACUUCAAAUCAAUUAUUC treated DNA pool, AGCAAUAAUUGAUUUGAAGUUGUAAUUCAAUUAUU Aggregated Drop Reaction, GGG (SEQ ID NO: 433) 5 day time point Seeded with hot alkali- 46 GGAAUAAUUUGAAAUUGGCAGUUAUUGUUCAAAU treated DNA pool, UAUUCUCCCAAAUUUGAACAAUAACUGCCAAUUUC Aggregated Drop Reaction, AAAUUUGGG (SEQ ID NO: 434) 5 day time point Seeded with hot alkali- 47 GGAAAAUUCAAAACUUUUCCGAAAAGUUUUUGAAA treated DNA pool, AUUCAAAACUUUUCGGAAAAGUUUUGAAUUUUGG Aggregated Drop Reaction, (SEQ ID NO: 435) 5 day time point Seeded with hot alkali- 48 GGAAUAUUAAAUACUUUAUUCUCCCAAUAUAAAGU treated DNA pool, AUUAAAUACUUUAUAUUGGGAGAAUAAAGUAUUUA Aggregated Drop Reaction, AUAUUGGG (SEQ ID NO: 436) 5 day time point Seeded with hot alkali- 49 GGAAAUAUUGGUAUUUAAUUUUUACUGUUUUUCU treated DNA pool, ACCAAUAUUUCCCAAAAAUUGGUAGAAAAACAGUA Aggregated Drop Reaction, AAAAUUAAAUACCAAUAUUUGGG (SEQ ID NO: 437) 5 day time point Seeded with hot alkali- 50 GGAAAAAUAAAUGAUAUGUUUCCAUCAUUUAUCAU treated DNA pool, UUAUUUUCCUUAAAAAUAAAUGAUAAAUGAUGGAA Aggregated Drop Reaction, ACAUAUCAUUUAUUUUUGG (SEQ ID NO: 438) 5 day time point Seeded with hot alkali- 51 GGAAAUUUCAAAGUUACAAGUCUCCGACUUUGAU treated DNA pool, UUUGACAAAUUUCAAAGUCGGAGACUUGUAACUU Aggregated Drop Reaction, UGAAAUUUGG (SEQ ID NO: 439) 5 day time point Seeded with hot alkali- 52 GGAAGAAUUUUGGUAGUGAAAGAUGCUACAAAUU treated DNA pool, CUUCGAAGAAUUUUUGUAGCAUCUUUCACUACCA Aggregated Drop Reaction, AAAUUCUUGGG (SEQ ID NO: 440) 5 day time point Seeded with hot alkali- 53 GGAAUAAAUCUUCAAUAAAUCCGAAGAUUUUAUUU treated DNA pool, UUCAAUAAAAUCUUCGGAUUUAUUGAAGAUUUAUU Aggregated Drop Reaction, GG (SEQ ID NO: 441) 5 day time point Seeded with hot alkali- 54 GGGAAAAUCAUCAAUCGGUUCCUCUGAUGAUUUU treated DNA pool, CCAAAUCAUCAGAGGAACCGAUUGAUGAUUUGGG Aggregated Drop Reaction, (SEQ ID NO: 442) 5 day time point Seeded with hot alkali- 55 GGGAAAAUUGGAAUCGAUACUCCUAUAUCCAAUU treated DNA pool, UUCCCCAAAAUUGGAUAUAGGAGUAUCGAUUCCA Aggregated Drop Reaction, AUUUUGG (SEQ ID NO: 443) 5 day time point Seeded with hot alkali- 56 GGAAAAUAUGAAUAUCAAUCCCCAUUCAUAUUUCA treated DNA pool, AAAAUAUGAAUGGGGAUUGAUAUUCAUAUUUUGG Aggregated Drop Reaction, (SEQ ID NO: 444) 5 day time point Seeded with hot alkali- 57 GGAUUAAUUCAAAUUAAUUAAUGGAAUUAAUUCAA treated DNA pool, AUUAAUUCCAUUAAUUAAUUUGAAUUAAUGG Aggregated Drop Reaction, (SEQ ID NO: 445) 5 day time point Seeded with hot alkali- 58 GGAAAAAUUCAAAUCAAGUAUCGAUUUGAAAUUCA treated DNA pool, AAUCGAUACUUGAUUUGAAUUUUGG Aggregated Drop Reaction, (SEQ ID NO: 446) 5 day time point Seeded with hot alkali- 59 GGAAAUUUGAAUUGCAACCAACGAUUCAAAUUCUC treated DNA pool, CCAAUUUGAAUCGUUGGUUGCAAUUCAAAUUGGG Aggregated Drop Reaction, (SEQ ID NO: 447) 5 day time point Seeded with hot alkali- 60 GGGAGGAGAUUCAAAUUUCAGAAGGACGAUUUGA treated DNA pool, AUUUCAGAUUCAAAUCGUCCUUCUGAAAUUUGAA Aggregated Drop Reaction, UCUGG (SEQ ID NO: 448) 5 day time point Seeded with hot alkali- 61 GGAAAAAAGUUCUAUUCAGUCCUAGACUUUUUUC treated DNA pool, UUCCAAAAGUCUAGGACUGAAUAGAACUUUUGGG Aggregated Drop Reaction, (SEQ ID NO: 449) 5 day time point Seeded with hot alkali- 62 GGAUUAUUUCUAGAUUAUUGAAAUAAUGAAAUAAC treated DNA pool, CCAUUAUUUCAUUAUUUCAAUAAUCUAGAAAUAAU Aggregated Drop Reaction, GGG (SEQ ID NO: 450) 5 day time point Seeded with hot alkali- 63 GGAGAAAUAUUCAUUCUCAUAUUCAAUAGCAUUG treated DNA pool, CAAUAUGAGAAUGAAUAUUGG (SEQ ID NO: 451) Aggregated Drop Reaction, 5 day time point Seeded with hot alkali- 64 GGAAAAUUUCUAAUAAUUCUAGAAAUUUCUAAUAA treated DNA pool, AUUUCUAGAAUUAUUAGAAAUUUUGG Aggregated Drop Reaction, (SEQ ID NO: 452) 5 day time point Seeded with hot alkali- 65 GGAAAUCAUUGGAAUUUUGUUGGCUUUCCAAUGA treated DNA pool, UUCCUCAUCAUCAUUGGAAAGCCAACAAAAUUCCA Aggregated Drop Reaction, AUGAUUUGG (SEQ ID NO: 453) 5 day time point Seeded with hot alkali- 66 GGAAUAAUUCAAAAUAAUUCUAUCUCAUUUUGAAA treated DNA pool, UAAUUCAAAAUGAGAUAGAAUUAUUUUGAAUUAUU Aggregated Drop Reaction, GG (SEQ ID NO: 454) 5 day time point Seeded with hot alkali- 67 GGAAUUCAAUUCAAAAGUUUCCUUUUGACUUUUG treated DNA pool, AAUUCAAUUCAAAAGUCAAAAGGAAACUUUUGAAU Aggregated Drop Reaction, UGAAUUGGG (SEQ ID NO: 455) 5 day time point Seeded with hot alkali- 68 GGAAAAUUUCAAACUACCAUUCCCUGUUUGAAAAU treated DNA pool, UUCAAACAGGGAAUGGUAGUUUGAAAUUUGGG Aggregated Drop Reaction, (SEQ ID NO: 456) 5 day time point Unseeded, Tube Reaction, 1 GGAACAUAAUGUUUGUUUCCACAUAAUGUUACAU 1 day time point GUGUGGAAACAUUAUUACACAUAAUGUUUCCACA CAUGUAACAUUAUGUGGAAACAAACAUUAUGUUG GG (SEQ ID NO: 457) Unseeded, Tube Reaction, 2 GGAAAAAUAUAAAUAUAAGAGAGUAUUUAUAUUUA 1 day time point GAAAAUAUAAAUACUCUCUUAUAUUUAUAUUUUGG (SEQ ID NO: 458) Unseeded, Tube Reaction, 3 GGAUUGAAUUCAAUUUCACUGAAUUCAGUGAAAU 1 day time point UCGAAUUUUGGAUUGAAUUCAAUUUCACUGAAUU CAGUGAAAUUCGAAUUUUGG (SEQ ID NO: 459) Seeded with DNA pool, 1 GGAAAAUUCAAUUCUAUCUAUUCAACAAUAGAAAA Tube Reaction, 1 day time UUCAAUUCUAUCUAUUGUUGAAUAGAUAGAAUUG point AAUUUGG (SEQ ID NO: 460) Seeded with DNA pool, 2 GGAAUUUUCAGAUAUUUAUUGCCUCUAUAUCUGA Tube Reaction, 1 day time UAAAUUUCAGAUAUAGAGGCAAUAAAUAUCUGAAA point UUUGG (SEQ ID NO: 461) Seeded with DNA pool, 3 GGGAAAAAUUCAAUUGAUAAUACAAUGUUUCCAUU Tube Reaction, 1 day time GAAUUUCAAAAAUUCAAUGGAAACAUUGUAUUAUC point AAUUGAAUUUUUGG (SEQ ID NO: 462) Seeded with DNA pool, 4 GGAAAAAUUCAAUGAUGCUUCGUUUCAUUGAAUU Tube Reaction, 1 day time CAAAAUUCAAGGAAACGAAGCAUCAUUGAAUUUUG point GGG (SEQ ID NO: 463) Seeded with DNA pool, 5 GGGGAAAAUUGAUAUUGCAGACUUUUUUUUCAAU Tube Reaction, 1 day time AUCAAAUUGAUAUUGAAAAAAAGUCUGCAAUAUCA point AUUUGG (SEQ ID NO: 464) Seeded with DNA pool, 6 GGGGAUGAAAUUCAAUUCGAGACGAAUUUCAUUU Tube Reaction, 1 day time CAAUGAAAUUCGUCUCGAAUUGAAUUUCAUUGGG point G (SEQ ID NO: 465) Seeded with DNA pool, 7 GGAAAAAAUCAAUUCAAUUCAAUUGAUUUUUGAAU Tube Reaction, 1 day time CAAUCCCAAAAAUCAAUUGAAUUGAAUUGAUUUUU point GGG (SEQ ID NO: 466) Seeded with DNase-treated 1 GGAUUAAAAUCAAAUGAUCCUAUUCUCCAUCAUUU DNA pool, Tube Reaction, 1 GAAUUAAAAUCAAAUGAUGGAGAAUAGGAUCAUUU day time point GAUUUUCGG (SEQ ID NO: 467) Seeded with DNase-treated 2 GGGGAAAAUUGAUUUUCAAUUCAAUUUCGAAAUU DNA pool, Tube Reaction, 1 GAUUUCUUUCAAUUUCGAAAUUGAAUUGAAAAUCA day time point AUUUUGGG (SEQ ID NO: 468) Seeded with DNase-treated 3 GGGGAAUAUUUCAUUUCUUAUAUCCAAUAUUUCC DNA pool, Tube Reaction, 1 GAAAUAUUUCCCAAUAUUUCGGAAAUAUUGGAUAU day time point AAGAAAUGAAAUAUUGGGG (SEQ ID NO: 469) Seeded with hot alkali- 1 GGAAUAAUAAAGGAUUCAAAUAUCAUUAUUAUACC treated DNA pool, Tube AAUAAUAAUGAUAUUUGAAUCCUUUAUUAUUGG Reaction, 1 day time point (SEQ ID NO: 470) Seeded with hot alkali- 2 GGUAUAAUAAUGAUAUUUGAAUCCUUUAUUAUUC treated DNA pool, Tube CCCAAUAAUAAAGGAUUCAAAUAUCAUUAUUAUUG Reaction, 1 day time point G (SEQ ID NO: 471) Seeded with hot alkali- 3 GGAAUAAUAAAGGAUUCAAAUAUCAUUAUUAUACC treated DNA pool, Tube AAUAAUAAUGAUAUUUAAUGAUAUUUGAAUCCUUU Reaction, 1 day time point AUUAUUGG (SEQ ID NO: 472) Seeded with hot alkali- 4 GGAAUAAUAAAGGAUUCAAAUAUCAUUAUUAUAAU treated DNA pool, Tube GAUAUUUGAAUCCUUUAUUAUUGG Reaction, 1 day time point (SEQ ID NO: 473) Unseeded, Tube Reaction, 1 GGAUGAAAUCUUUCAGACGUUUUCUCUGAUUUUU 5 day time point UGUCCAAGAAAUCAGAGAAAACGUCUGAAAGAUUU CUUGG (SEQ ID NO: 474) Unseeded, Tube Reaction, 2 GGAUGAAAUCUUUCAGACGUUUUCUCUGAUUUUU 5 day time point UUUUCAGAGAAAACGUCUGAAAGAUUUCUUGG (SEQ ID NO: 475) Unseeded, Tube Reaction, 3 GGAAAAUUUCUAUAUCACAUUACAUAUGUAAUUUU 5 day time point CUAUAUUACAUAUGUAAUGUGAUAUAGAAAUUUUG G (SEQ ID NO: 476) Unseeded, Tube Reaction, 4 GGAAAAAUAAAUCUUUAUCAUUUUACCUGAAGAUU 5 day time point UAUGAAAUAAAUCUUCAGGUAAAAUGAUAAAGAUU UAUUUUGG (SEQ ID NO: 477) Unseeded, Tube Reaction, 5 GGAAGAAUUAAUGGUAUUUCUAUUAUAAUUUGCA 5 day time point AAUUAUAAUAGAAAUACCAUUAAUUCUUGG (SEQ ID NO: 478) Unseeded, Tube Reaction, 6 GGAAAAAUUCAAUGAAGCGCUUCCUUGAAUUUGA 5 day time point AAGUGAAGAAAUUCAAUGAAGCGCUUCAUUGAAU UUUGG (SEQ ID NO: 479) Unseeded, Tube Reaction, 7 GGACAAAAAAUCAGAGAAAACGUCUGAAAGAUUUC 5 day time point AUCCCCAAGAAAUCUUUCAGACGUUUUUCUCUGA UUUCUUGGG (SEQ ID NO: 480) Unseeded, Tube Reaction, 8 GGAAGAAUUAAUGGUAUUUCUAUUAUAAUUUGCG 5 day time point GAUAAAAAAUUGUGCAAAUUAUAAUAGAAAUACCA UUAAUUCUUGG (SEQ ID NO: 481) Unseeded, Tube Reaction, 9 GGAUGAAAUCUUUCAGACGUUUUCUCUGAUUUUU 5 day time point UUGUCCAAGAAAUCAGAGAAAAAAAUCAGAGAAAA CGUCUGAAAGAUUUCUUGG (SEQ ID NO: 482) Unseeded, Tube Reaction, 10 GGAUGAAAUCUUUCAGACGUUUUCUCUGAUUAAA 5 day time point UCAGAGAAAAAACGUCUGAAAGAUUUCUUGG (SEQ ID NO: 483) Unseeded, Tube Reaction, 11 GGAAGAAUUAAUGGUAUUUCUAUUAUAAUAGAAAU 5 day time point ACCAUUAAUUCAUGG (SEQ ID NO: 484) Seeded with hot alkali- 1 GGAAUAUUUCUUCAAUUCAACAUGAAAUAAUAUUC treated DNA pool, Tube CAAUAUUUCAUGUUGAAUUGAAGAAAUAUUGG Reaction, 5 day time point (SEQ ID NO: 485) Seeded with hot alkali- 2 GGAUAAUAAUAAUUGAAUUCCAUUUUCCAAUUAUU treated DNA pool, Tube AUCCAAAUAUAAUAAUUGGAAAAUGGAAUUCAAUU Reaction, 5 day time point AUUAUUUUGG (SEQ ID NO: 486) Seeded with hot alkali- 3 GGAUAAUUCUAAUAGUCAAUUCUCCCUAUUUAGAA treated DNA pool, Tube UUAUAAUAUAUAUUAUAUAUAAUUCUAAUAGGGGA Reaction, 5 day time point GAAUUGACUAUUAGAAUUAUGG (SEQ ID NO: 487) Seeded with hot alkali- 4 GGAAAAUUAUAGUUCUACUUCGAUAUUUGAAAACU treated DNA pool, Tube AUAAAAUUCCAAAUUAUAGUUUUCAAAUAUCGAAG Reaction, 5 day time point UAGAACUAUAAUUUGGG (SEQ ID NO: 488) Seeded with hot alkali- 5 GGAAAUUUCAAUAUGAAUAUUUUGUUUCGUAUUU treated DNA pool, Tube GAUUUUAAAUUUCAAUACGAAACAAAAUAUUCAUA Reaction, 5 day time point UUGAAAUUUGG (SEQ ID NO: 489) Seeded with hot alkali- 6 GGGAGAUUAUACUCAUUCGAACCCAGAGUAUAUG treated DNA pool, Tube AUUAUACUCUGGGUUCGAAUGAGUAUAAUCAUGG Reaction, 5 day time point (SEQ ID NO: 490) Seeded with hot alkali- 7 GGAAAAUUUCAAAUUCAAGCCUGAAUGAAAUUUUU treated DNA pool, Tube CAAAUUCAUUCAGGCUUGAAUUUGAAAUUUUGG Reaction, 5 day time point (SEQ ID NO: 491) Seeded with hot alkali- 8 GGAAUAUUUCUUCAAUUCAAUGUUGAAUUGAAGA treated DNA pool, Tube AAUAUUGG (SEQ ID NO: 492) Reaction, 5 day time point Seeded with hot alkali- 9 GGAAAAUAUAAUUCAUAUUGGAAGACAGAAUUAUU treated DNA pool, Tube UAUACAAAUAUAAUUCUGUCUUCCAAUAUGAAUUA Reaction, 5 day time point UAUUUGG (SEQ ID NO: 493) Seeded with hot alkali- 10 GGAAAAAUUAAACAAAAAUGCUUUGUAUGUUUAAU treated DNA pool, Tube UUUCAUCCAAAAUUAAACAUACAAAGCAUUUUUGU Reaction, 5 day time point UUAAUUUUGGG (SEQ ID NO: 494) Seeded with hot alkali- 11 GGAAAAAUAAUCGAAAUAUUUUGAUCGAUUAUUUU treated DNA pool, Tube GAUUAAGUUCAAAAAUAAUCGAUCAAAAUAUUUCG Reaction, 5 day time point AUUAUUUUGGG (SEQ ID NO: 495) Seeded with hot alkali- 12 GGGAAAAUAUUUGUUUCAGAUCUCCAAAUAUUUG treated DNA pool, Tube CCAAAUAUUUGGAGAUCUGAAACAAAUAUUUGG Reaction, 5 day time point (SEQ ID NO: 496) Seeded with hot alkali- 13 GGAAAAUUUGAAUUCAAUUCUCUGAAGAAUUCAAA treated DNA pool, Tube UUUUGAAUUCUUCAGAGAAUUGAAUUCAAAUUUG Reaction, 5 day time point GGGG (SEQ ID NO: 497) Seeded with hot alkali- 14 GGAAUUAAUAUUAUUCAUAUUCAAUUGAUGAAUUA treated DNA pool, Tube AUAUUAUUCAUCAAUUGAAUAUGAAUAAUAUUAAU Reaction, 5 day time point UGG (SEQ ID NO: 498) Seeded with hot alkali- 15 GGAUAUAAUAGUACAUCUUCAAUUCCUACUAUUAA treated DNA pool, Tube UAUCCAAUAAUAGUAGGAAUUGAAGAUGUACUAUU Reaction, 5 day time point AUUGG (SEQ ID NO: 499) NB: Short 5′ and 3′ base extensions (of one or a few bases) may be present in the sequences for reasons discussed in the text.

TABLE 3 Oligonucleotide sequences used in our study. Oligo name Sequence Notes AF-NJ-269 /5rApp/NNNNNNNNAGATCGGAAGAGCACACGICT RNase-free HPLC /3ddC/ (SEQ ID NO: 500) purified, /5rApp/ is the IDT code for 5′ Adenylation, Ns are machine mixed, /3ddC/ is the IDT code for 3′ Dideoxycytidine AF-NJ-200 CCAAAATTNGTANGTAGTAGTACNAAATTTTGGAA Standard desalting, AATTTNGTACTACTACNTACNAATTTTCCTATAGT ordered as DNA GAGTCGTATTANNNNTAATACGACTCACTATA ultramer, Ns are (SEQ ID NO: 501) machine mixed AF-NJ-201 CCAAAATTANTAGNTAGTAGTANTAAATTTTGGAA Standard desalting, AATTTANTACTACTANCTANTAATTTTCCTATAGTG ordered as DNA AGTCGTATTANNNNTAATACGACTCACTATA ultramer, Ns are (SEQ ID NO: 502) machine mixed AF-JTG-11 CCAAAATTAGTAGGTANTAGTANTAAATTTTGNAA Standard desalting, AATTTANTACTANTACCTACTAATTTTCCTATAGTG ordered as DNA AGTCGTATTANNNNTAATACGACTCACTATA ultramer (SEQ ID NO: 503) AF-JTG-13 CCAAAATTTNAAGATCAGGGCTTNAAATTTTGNAA Standard desalting, AATTTNAAGCCCTGATCTTNAAATTTTCCTATAGT ordered as DNA GAGTCGTATTANNNNTAATACGACTCACTATA ultramer (SEQ ID NO: 504) AF-KLA-67 AATGATACGGCGACCACCGAGATCTACACTATAG CCTACACTCTTTCCCTACACGACGCTCTTCCGAT CT (SEQ ID NO: 505) AF-KLA-68 AATGATACGGCGACCACCGAGATCTACACATAGA GGCACACTCTTTCCCTACACGACGCTCTTCCGAT CT (SEQ ID NO: 506) AF-KLA-69 AATGATACGGCGACCACCGAGATCTACACCCTAT CCTACACTCTTTCCCTACACGACGCTCTTCCGAT CT (SEQ ID NO: 507) AF-KLA-70 AATGATACGGCGACCACCGAGATCTACACGGCTC TGAACACTCTTTCCCTACACGACGCTCTTCCGAT CT (SEQ ID NO: 508) AF-KLA-71 AATGATACGGCGACCACCGAGATCTACACAGGC GAAGACACTCTTTCCCTACACGACGCTCTTCCGA TCT (SEQ ID NO: 509) AF-KLA-72 AATGATACGGCGACCACCGAGATCTACACTAATC TTAACACTCTTTCCCTACACGACGCTCTTCCGATC T (SEQ ID NO: 510) AF-KLA-73 AATGATACGGCGACCACCGAGATCTACACCAGG ACGTACACTCTTTCCCTACACGACGCTCTTCCGA TCT (SEQ ID NO: 511) AF-KLA-74 AATGATACGGCGACCACCGAGATCTACACGTACT GACACACTCTTTCCCTACACGACGCTCTTCCGAT CT (SEQ ID NO: 512) AF-ZF-838 CAAGCAGAAGACGGCATACGAGATCGAGTAATGT GACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 513) AF-ZF-839 CAAGCAGAAGACGGCATACGAGATTCTCCGGAG TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 514) AF-ZF-840 CAAGCAGAAGACGGCATACGAGATAATGAGCGG TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 515) AF-ZF-841 CAAGCAGAAGACGGCATACGAGATGGAATCTCG TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 516) AF-ZF-842 CAAGCAGAAGACGGCATACGAGATTTCTGAATGT GACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 517) AF-ZF-843 CAAGCAGAAGACGGCATACGAGATACGAATTCGT GACTGGAGTTCAGACGTGTGCTCTTCCGATCT (SEQ ID NO: 518)

TABLE 4 Sequences of RNA species described in FIG. 8. Round 2 RNA pool Reference sequence for most abundant RNA species 2A GGAAAAUUUCAAACAUUAUGUUGUAAUUUGUUUGAAAAUUUCAAACAAAUUACAA CAUAAUGUUUGAAAUUUUGGGGGGAAAAU (SEQ ID NO: 519) 2B CCCAAUAUCAUCAAUUGCUGACGAAGAUGAUAUUGAUAAUAUCAUCUUCGUCAG CAAUUGAUGAUAUU (SEQ ID NO: 520) 2C GGAAAAUCAAUGACUGGUCAAUCUCAUUGAUUUUUGAAAUCAAUGAGAUUGACC AGUCAUUGAUUUU (SEQ ID NO: 521) NB: (i) Short 5′ and 3′ base extensions (of one or a few bases) may be present in the sequences for reasons discussed in the text. (ii) Sequences may not be full-length because particular truncated cDNAs or prematurely terminated T7 products were predominant in the sequenced pool.

TABLE 5 Brief description of the functionality of the code deposited on GitHub. Functionality Code Name (brief description) Notes trimmer_20180216.py Adapter trimming analyzer.py Obtaining a list of (i) Checks that for each retained sequence, unique sequences both paired-end reads perfectly match to (with associated minimize effects from sequencing errors, (ii) counts) from paired- Stores two counts for each sequence (1. Non- end read data redundant UMI count: # unique molecular identifiers associated with sequence, 2. Possibly redundant UMI count: total # counts of sequence) denovoClustering_ver10_20180228.py Unsupervised (i) Groups sequences into clusters such that classification of no sequence stretch of 20 nucleotides is sequences shared between clusters, (ii) Within each cluster, sequences are further grouped into subclusters. Reference sequences for subclusters have more than 1 sequence variant every 20 bases (on average) with respect to each other. (iii) Definition of reference sequences for subclusters: Sequences are parsed in decreasing order of counts in the code. A subcluster is thus initially defined by a reference sequence which is the most abundant sequence representing the information content of the subcluster. smithWaterman_collapser_20180301.py Aligning reference (i) Results in a list of unique reference sequences for all sequences defining the RNA species for a subclusters (across sequenced pool, (ii) Unique reference all clusters) with sequences have more than 1 sequence respect to each other variant every 10 bases (on average) with respect to each other. collapsingEndHeterogeneityAlignments_ Pruning potential 5′ 20180301.py and 3′ extra bases from reference sequences alignmentQuantification_ver2_ Quantifying relative abundance of RNA species in a 20180305.py sequenced pool using reference sequences for alignment finalQuantification_phylipFitch_ver2_ Creating a distance (i) Used for FIG. 1D 20180315.py tree between reference sequences based on number of sequence variants between the references 2dPlots_Final_ver4_20190503.py Calculating various (i) Used for FIG. 1E-G metrics for RNA species; automated detection of 2-way and 4-way repeats in reference sequences *Notes regarding the sequences reported in FIG. 1 and Table 1: (i) Short 5′ and 3′ base extensions (of one or a few bases) may be present in the sequences for reasons discussed in the text. (ii) A few sequences may not be full-length because particular truncated cDNAs or prematurely terminated T7 products were predominant in the sequenced pool.

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1. A method of amplifying RNA comprising replicating the RNA in a reaction mixture comprising: an RNA polymerase; a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, or analogues or derivatives thereof; and an RNA template comprising (i) a 2-way repeat configuration comprising a first inverted repeat, and (ii) a 4-way repeat configuration comprising a second inverted repeat that is shorter than the first inverted repeat, wherein each arm of the 2-way repeat comprises the second inverted repeat.
 2. The method of claim 1, wherein the RNA polymerase is a bacteriophage transcription polymerase.
 3. The method of claim 2, wherein the bacteriophage transcription polymerase is a T7 bacteriophage RNA polymerase.
 4. (canceled)
 5. The method of claim 1, wherein the reaction mixture contains no DNA.
 6. The method of claim 1, wherein the RNA template ranges from 50 to 120 nucleotides in length.
 7. The method of claim 1, wherein each repeat region within the 2-way repeat configuration ranges from 10 to 60 nucleotides in length or about 20% to about 50% of the total length of the replicating RNA.
 8. The method of claim 1, wherein each repeat region within the 4-way repeat configuration ranges from 5 to 25 nucleotides in length or about 5% to about 20% of the total length of the replicating RNA.
 9. The method of claim 1, wherein the replicating RNA in the reaction comprises a G RNA strand comprising two G bases at or close to a 5′ end and two G bases at or close to a 3′ end, and a complementary C RNA strand comprising two C bases at or close to a 5′ end and two C bases at or close to a 3′ end.
 10. The method of claim 9, further comprising adding at least one base to the 3′ end of the G RNA strand or the C RNA strand. 11-12. (canceled)
 13. The method of claim 1, wherein the RNA template is linear.
 14. The method of claim 1, wherein the RNA template is provided by a DNA seed, wherein the RNA template for replication is generated by transcription of the DNA seed.
 15. The method of claim 14, wherein the DNA seed comprises a nucleotide sequence of interest and a 4-way repeat unit.
 16. The method of claim 15, wherein the DNA seed is added to the reaction mixture such that the RNA polymerase generates a first RNA comprising the 4-way repeat unit by transcription of the DNA seed.
 17. The method of claim 16, further comprising carrying out a first round of 3′-extension of the first RNA to produce a second RNA comprising a second 4-way repeat unit; and carrying out a second round of 3′-extension of the second RNA to produce the RNA template comprising the 4-way repeat configuration.
 18. The method of claim 1, wherein a single RNA or a plurality of RNAs are replicated in the reaction mixture.
 19. The method of claim 18, wherein the plurality of RNAs are RNA variants.
 20. The method of claim 18, wherein the method is performed in a microfluidic device comprising a droplet generator and further comprises partitioning the plurality of RNAs into a plurality of droplets and replicating the RNA using digital droplet RNA replication. 21-26. (canceled)
 27. The method of claim 1, further comprising using the amplified RNA for RNA interference, sequencing, expression profiling, a vaccine, or directed evolution of RNA aptamers without intermediate conversion to DNA.
 28. An RNA template for RNA replication by an RNA polymerase comprising a nucleotide sequence selected from Tables 1, 2, or 4, or a sequence having at least 80% identity to a nucleotide sequence selected from Tables 1, 2, or
 4. 29-30. (canceled)
 31. A composition for generating replicating RNA templates comprising: a) an RNA polymerase; b) a DNA seed, wherein the DNA seed comprises a nucleotide sequence of interest and a 4-way repeat unit; and c) a set of ribonucleoside triphosphates comprising ATP, CTP, GTP, and UTP, or analogues or derivatives thereof.
 32. (canceled) 